diff --git a/.github/actions/dependencies/action.yml b/.github/actions/dependencies/action.yml index c9ed6162d..71ca20603 100644 --- a/.github/actions/dependencies/action.yml +++ b/.github/actions/dependencies/action.yml @@ -3,8 +3,8 @@ description: Install UV and dependencies runs: using: composite steps: - - name: Install uv - uses: astral-sh/setup-uv@v4 + - name: Set up uv + uses: astral-sh/setup-uv@v7 - name: Install dependencies shell: bash diff --git a/.github/actions/uv/action.yml b/.github/actions/uv/action.yml index 07d45b0d6..121fc243f 100644 --- a/.github/actions/uv/action.yml +++ b/.github/actions/uv/action.yml @@ -3,7 +3,7 @@ description: Install UV runs: using: composite steps: - - name: Set up UV - uses: astral-sh/setup-uv@v3 + - name: Set up uv + uses: astral-sh/setup-uv@v7 with: enable-cache: true \ No newline at end of file diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 42baa2574..54c633a0d 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -16,4 +16,18 @@ updates: groups: actions: patterns: - - "github-actions" + - "*" + + - package-ecosystem: "uv" + directory: "/" + schedule: + interval: "monthly" + commit-message: + prefix: "deps(dependabot):" + open-pull-requests-limit: 1 + rebase-strategy: "auto" + groups: + python-all: + patterns: + - "*" + diff --git a/.github/workflows/add-issue-to-project.yml b/.github/workflows/add-issue-to-project.yml index 646a0d610..60b4d8bd5 100644 --- a/.github/workflows/add-issue-to-project.yml +++ b/.github/workflows/add-issue-to-project.yml @@ -10,7 +10,7 @@ jobs: name: Add issue to project runs-on: ubuntu-latest steps: - - uses: actions/add-to-project@v1.0.2 + - uses: actions/add-to-project@v2.0.0 with: project-url: https://github.com/orgs/mesoscope/projects/1 github-token: ${{ secrets.PROJECT_PAT }} diff --git a/.github/workflows/analyze.yml b/.github/workflows/analyze.yml index 66feb8e46..eed5b041e 100644 --- a/.github/workflows/analyze.yml +++ b/.github/workflows/analyze.yml @@ -15,7 +15,7 @@ jobs: python-version: [3.11] os: [ubuntu-latest] steps: - - uses: actions/checkout@v4.2.2 + - uses: actions/checkout@v6 - uses: ./.github/actions/dependencies - name: Pack test recipe run: | @@ -27,7 +27,7 @@ jobs: - name: Run analysis code run: uv run analyze -r cellpack/tests/recipes/v2/test_spheres.json -a cellpack/tests/analysis-configs/PR_analysis_config.json -p cellpack/tests/outputs/test_spheres/spheresSST - name: Upload results - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@v7 with: name: results path: cellpack/tests/outputs/test_spheres/ @@ -35,41 +35,58 @@ jobs: runs-on: ubuntu-latest needs: [Analyze] steps: - - uses: actions/checkout@v4.2.2 + - uses: actions/checkout@v6 - name: Configure AWS credentials for dependabot if: ${{ github.actor == 'dependabot[bot]' }} - uses: aws-actions/configure-aws-credentials@v4 + uses: aws-actions/configure-aws-credentials@v6 with: aws-access-key-id: ${{ secrets.DEPENDABOT_AWS_ACCESS_KEY_ID }} aws-secret-access-key: ${{ secrets.DEPENDABOT_AWS_SECRET_ACCESS_KEY }} aws-region: us-west-2 - name: Configure AWS credentials if: ${{ github.actor != 'dependabot[bot]' }} - uses: aws-actions/configure-aws-credentials@v4 + uses: aws-actions/configure-aws-credentials@v6 with: aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} aws-region: us-west-2 - - uses: actions/download-artifact@v6 + - uses: actions/download-artifact@v8 with: name: results path: ./results - name: Copy files to results bucket run: aws s3 cp ./results s3://cellpack-results/${{ github.ref_name }}/ --recursive --acl public-read - - uses: iterative/setup-cml@v2 - with: - vega: false # we only use CML to post markdown reports, so disable vega to skip extra npm installs - name: Update comment for dependabot - if: ${{ github.actor == 'dependabot[bot]' }} + if: ${{ github.event_name == 'pull_request' && github.actor == 'dependabot[bot]' }} env: - REPO_TOKEN: ${{ secrets.DEPENDABOT_TOKEN }} + GH_TOKEN: ${{ secrets.DEPENDABOT_TOKEN }} run: | - cml comment update --watermark-title="{workflow} report" ./results/analysis_report.md --target=pr + MARKER="" + COMMENT_BODY="${MARKER} + $(cat ./results/analysis_report.md)" + EXISTING_COMMENT_ID=$(gh api "/repos/${{ github.repository }}/issues/${{ github.event.pull_request.number }}/comments" --jq ".[] | select(.body | contains(\"${MARKER}\")) | .id" | head -1) + if [ -n "$EXISTING_COMMENT_ID" ]; then + echo "Updating existing comment with ID: $EXISTING_COMMENT_ID" + echo "$COMMENT_BODY" | gh api -X PATCH "/repos/${{ github.repository }}/issues/comments/$EXISTING_COMMENT_ID" -F body=@- + else + echo "Creating new comment" + echo "$COMMENT_BODY" | gh pr comment ${{ github.event.pull_request.number }} --body-file - + fi cat ./results/analysis_report.md - name: Update comment for PR - if: ${{ github.actor != 'dependabot[bot]' }} + if: ${{ github.event_name == 'pull_request' && github.actor != 'dependabot[bot]' }} env: - REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} run: | - cml comment update --watermark-title="{workflow} report" ./results/analysis_report.md --target=pr + MARKER="" + COMMENT_BODY="${MARKER} + $(cat ./results/analysis_report.md)" + EXISTING_COMMENT_ID=$(gh api "/repos/${{ github.repository }}/issues/${{ github.event.pull_request.number }}/comments" --jq ".[] | select(.body | contains(\"${MARKER}\")) | .id" | head -1) + if [ -n "$EXISTING_COMMENT_ID" ]; then + echo "Updating existing comment with ID: $EXISTING_COMMENT_ID" + echo "$COMMENT_BODY" | gh api -X PATCH "/repos/${{ github.repository }}/issues/comments/$EXISTING_COMMENT_ID" -F body=@- + else + echo "Creating new comment" + echo "$COMMENT_BODY" | gh pr comment ${{ github.event.pull_request.number }} --body-file - + fi cat ./results/analysis_report.md diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml index d32349135..1c8398d91 100644 --- a/.github/workflows/build-docs.yml +++ b/.github/workflows/build-docs.yml @@ -17,14 +17,14 @@ jobs: if: ${{ !contains(github.event.head_commit.message, 'Bump version') }} runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4.2.2 + - uses: actions/checkout@v6 with: persist-credentials: false - uses: ./.github/actions/dependencies - name: Setup Pages - uses: actions/configure-pages@v5 + uses: actions/configure-pages@v6 - name: Generate Docs run: | @@ -33,7 +33,7 @@ jobs: - name: Upload artifact id: deployment - uses: actions/upload-pages-artifact@v4 + uses: actions/upload-pages-artifact@v5 with: path: docs/_build/html/ @@ -50,5 +50,5 @@ jobs: steps: - name: Deploy to GitHub Pages id: deployment - uses: actions/deploy-pages@v4 + uses: actions/deploy-pages@v5 diff --git a/.github/workflows/cache-dependencies.yml b/.github/workflows/cache-dependencies.yml index 548d29557..b95c9b410 100644 --- a/.github/workflows/cache-dependencies.yml +++ b/.github/workflows/cache-dependencies.yml @@ -14,5 +14,5 @@ jobs: dependencies: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@v6 - uses: ./.github/actions/dependencies \ No newline at end of file diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index afa36e380..8c04e2fc1 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -30,19 +30,19 @@ jobs: os: [ubuntu-latest, windows-latest, macOS-latest] steps: - - uses: actions/checkout@v4.2.2 + - uses: actions/checkout@v6 - uses: ./.github/actions/dependencies - name: Test with pytest run: | uv run pytest --cov cellpack/tests/ - name: Upload codecov - uses: codecov/codecov-action@v5 + uses: codecov/codecov-action@v6 lint: runs-on: ubuntu-latest if: ${{ !contains(github.event.head_commit.message, 'Bump version') }} steps: - - uses: actions/checkout@v4.2.2 + - uses: actions/checkout@v6 - uses: ./.github/actions/dependencies - name: Lint with flake8 run: | @@ -62,7 +62,7 @@ jobs: id-token: write steps: - - uses: actions/checkout@v4.2.2 + - uses: actions/checkout@v6 - uses: ./.github/actions/dependencies - name: Publish to PyPI run: uv publish diff --git a/.github/workflows/cleanup-aws.yml b/.github/workflows/cleanup-aws.yml index ba4d10d22..e2f402baf 100644 --- a/.github/workflows/cleanup-aws.yml +++ b/.github/workflows/cleanup-aws.yml @@ -9,9 +9,9 @@ jobs: cleanup: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4.2.2 + - uses: actions/checkout@v6 - name: Configure AWS credentials - uses: aws-actions/configure-aws-credentials@v4 + uses: aws-actions/configure-aws-credentials@v6 with: aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} diff --git a/.github/workflows/cleanup-firebase.yml b/.github/workflows/cleanup-firebase.yml deleted file mode 100644 index ec939d5b7..000000000 --- a/.github/workflows/cleanup-firebase.yml +++ /dev/null @@ -1,22 +0,0 @@ -name: Cleanup Firebase Metadata - -on: - schedule: - - cron: "24 18 * * 1" # Runs at 18:24 UTC every Monday - -jobs: - cleanup: - runs-on: ${{ matrix.os }} - strategy: - matrix: - python-version: [3.11] - os: [ubuntu-latest, windows-latest, macOS-latest] - steps: - - uses: actions/checkout@v4.2.2 - - uses: ./.github/actions/dependencies - - name: Cleanup Firebase Metadata - env: - FIREBASE_TOKEN: ${{ secrets.FIREBASE_TOKEN }} - FIREBASE_EMAIL: ${{ secrets.FIREBASE_EMAIL }} - run: | - uv run python cellpack/bin/cleanup_tasks.py diff --git a/.github/workflows/make-requirements.yml b/.github/workflows/make-requirements.yml deleted file mode 100644 index a0b989ee1..000000000 --- a/.github/workflows/make-requirements.yml +++ /dev/null @@ -1,106 +0,0 @@ -name: Make requirements files - -on: - workflow_dispatch: - push: - branches: - - main - paths: - - "uv.lock" - -jobs: - make-requirements: - runs-on: ${{ matrix.os }} - strategy: - matrix: - os: [ubuntu-latest, macOS-latest, windows-latest] - - steps: - - uses: actions/checkout@v4 - - name: Install uv - uses: astral-sh/setup-uv@v4 - - - name: Generate requirements.txt - shell: bash - run: | - case "${{ matrix.os }}" in - "ubuntu-latest") - export PLATFORM="linux" - ;; - "macOS-latest") - export PLATFORM="macos" - ;; - "windows-latest") - export PLATFORM="windows" - ;; - esac - - rm -rf requirements/* - mkdir -p requirements/$PLATFORM - uv export --no-hashes --format requirements-txt --output-file requirements/$PLATFORM/requirements.txt - - - name: Get platform variable - id: platform - shell: bash - run: | - case "${{ matrix.os }}" in - "ubuntu-latest") - echo "platform=linux" >> $GITHUB_OUTPUT - ;; - "macOS-latest") - echo "platform=macos" >> $GITHUB_OUTPUT - ;; - "windows-latest") - echo "platform=windows" >> $GITHUB_OUTPUT - ;; - esac - - - name: Upload requirements files - uses: actions/upload-artifact@v4 - with: - name: ${{ steps.platform.outputs.platform }}-requirements - path: requirements/${{ steps.platform.outputs.platform }} - - open-PR: - needs: [make-requirements] - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - name: Download linux requirements files - uses: actions/download-artifact@v6 - with: - name: linux-requirements - path: requirements/linux - - - name: Download windows requirements files - uses: actions/download-artifact@v6 - with: - name: windows-requirements - path: requirements/windows - - - name: Download macOS requirements files - uses: actions/download-artifact@v6 - with: - name: macos-requirements - path: requirements/macos - - - name: Clean-up CRLF - shell: bash - run: find requirements -type f -exec sed -i 's/\r//g' {} \; - - - name: Get timestamp - id: timestamp - run: echo "timestamp=$(date +'%Y-%m-%d_%H-%M')" >> $GITHUB_OUTPUT - - - name: Create Pull Request - uses: peter-evans/create-pull-request@v7 - with: - base: main - title: admin/requirements-update_${{ steps.timestamp.outputs.timestamp }} - body: Updating requirements.txt. - - Due to some [challenges](https://github.com/peter-evans/create-pull-request/blob/main/docs/concepts-guidelines.md#triggering-further-workflow-runs), - with getting this PR to trigger the tests, please manually close and re-open this PR. - branch: admin/requirements-update_${{ steps.timestamp.outputs.timestamp }} - commit-message: Updating requirements.txt after change to `uv.lock` was pushed to `main` - delete-branch: true \ No newline at end of file diff --git a/README.md b/README.md index b35f7c2b9..2db8c1d51 100644 --- a/README.md +++ b/README.md @@ -6,10 +6,12 @@ An algorithm to pack molecular recipes +**Try cellPACK online:** [cellpack.allencell.org](https://cellpack.allencell.org) + ## Installation > [!NOTE] -> These are the basic installation steps. However, our recommendation for developers is to install using `uv`. See advanced installation instructions [here](./docs/INSTALL.md). +> These are the basic installation steps. However, our recommendation for developers is to install using `uv`. See advanced installation instructions [here](./docs/INSTALLATION.md). 1. Install Python 3.11 and `git`. Update pip at least to `24.0.0`. 2. Clone this git repository. @@ -17,22 +19,77 @@ An algorithm to pack molecular recipes git clone git@github.com:mesoscope/cellpack.git cd cellpack ``` -1. Create a new virtual environment and activate it. +3. Create a new virtual environment and activate it. ```bash python -m venv .venv source .venv/bin/activate ``` -1. Install the required packages for your operating system. Replace `linux` with `macos` or `windows` as appropriate. +4. Install the package and its dependencies from `pyproject.toml`. ```bash pip install --upgrade pip -pip install -r requirements/linux/requirements.txt pip install -e . ``` ## Pack example recipes -1. v1: `pack -r examples/recipes/v1/NM_Analysis_FigureB1.0.json` -2. v2: `pack -r examples/recipes/v2/spheres_in_a_box.json` -3. Pack from remote server: `pack -r github:recipes/NM_Analysis_FigureB1.0.json ` + +cellPACK supports two recipe formats: **v1** (legacy) from the original publication, and **v2** (modern) with improved structure. We recommend starting with **v2** for new recipes. + +### Recipe Format Versions + +#### v1 Recipes (Legacy Format) +**v1 recipes** use the original schema from the [Nature Methods publication](https://www.nature.com/articles/nmeth.3204). These recipes feature: +- Explicit parameter definitions for all ingredients +- Backward compatibility with the original cellPACK publication examples + +**Example v1 recipes:** +- `NM_Analysis_FigureB1.0.json` - Blood plasma mesoscale model from the Nature Methods publication +- `BloodPlasma_noHIV_1.0_2D.json` - 2D blood plasma model +- `partner_packing.json` - Example of molecular partner binding + +**Run a v1 recipe:** +```bash +pack -r examples/recipes/v1/NM_Analysis_FigureB1.0.json +``` + +![Blood Plasma Model Result](docs/images/nm_analysis_figure_b1_res.png) + +#### v2 Recipes (Modern Format) +**v2 recipes** use a modernized schema with improved structure and features: +- Cleaner organization with `objects` and `composition` sections +- Object inheritance system for efficient recipe authoring +- Better support for complex cellular environments + +**Example v2 recipes:** +- `spheres_in_a_box.json` - Simple 3D multi-sphere packing (great for getting started) +- `peroxisome.json` - Peroxisome organelle model +- `er_peroxisome.json` - Endoplasmic reticulum with peroxisomes +- `vector_gradient.json` - Demonstrates gradient-based ingredient distributions +- `partner_packing.json` - Molecular partner interactions + +**Run a v2 recipe:** +```bash +pack -r examples/recipes/v2/spheres_in_a_box.json +``` + +![Multi-Sphere Result](docs/images/spheres_in_a_box_res.png) + +### Remote Recipe Loading +You can also load recipes directly from remote servers: +```bash +pack -r github:recipes/NM_Analysis_FigureB1.0.json +``` + +### Config Files +Config files control packing behavior and simulation parameters including: +- **Place methods** - Algorithm used for ingredient placement (e.g., `jitter`, `spheresSST`) +- **Output formats** - Save options for results and analysis +- **Grid settings** - Spatial grid parameters for collision detection +- **Debugging options** - Visualization and diagnostic tools + +**Using a config file:** +```bash +pack -r examples/recipes/v2/spheres_in_a_box.json -c examples/packing-configs/debug.json +``` **Stable Release:** `pip install cellpack`
**Development Head:** `pip install git+https://github.com/mesoscope/cellpack.git` @@ -49,6 +106,6 @@ See [CONTRIBUTING.md](./docs/CONTRIBUTING.md) for information related to develop cellPACK uses AWS and Firebase Firestore as remote databases to store packing results and recipes. Follow [ setup instructions](./docs/REMOTE_DATABASES.md) for access. ## Docker -cellPACK can be run in Docker containers for both AWS ECS and AWS Batch. Follow the [instructions](./docs/DOCKER.md) to set up the Docker environment. +cellPACK can be run in Docker containers for running the server on AWS ECS. Follow the [instructions](./docs/DOCKER.md) to set up the Docker environment. **MIT license** \ No newline at end of file diff --git a/cellpack/autopack/AWSHandler.py b/cellpack/autopack/AWSHandler.py index 3fff0c649..6e9bbe067 100644 --- a/cellpack/autopack/AWSHandler.py +++ b/cellpack/autopack/AWSHandler.py @@ -146,7 +146,7 @@ def save_file_and_get_url(self, file_path): if self.is_url_valid(base_url): return file_name, base_url except NoCredentialsError as e: - print(f"AWS credentials are not configured, details:{e}") + logging.warning(f"AWS credentials are not configured: {e}") return None, None return None, None diff --git a/cellpack/autopack/Analysis.py b/cellpack/autopack/Analysis.py index 3c727ceae..c37babf0d 100644 --- a/cellpack/autopack/Analysis.py +++ b/cellpack/autopack/Analysis.py @@ -4,6 +4,7 @@ @author: ludo """ + import concurrent.futures import json import logging diff --git a/cellpack/autopack/BaseGrid.py b/cellpack/autopack/BaseGrid.py index efcab8ab4..a1fac5940 100644 --- a/cellpack/autopack/BaseGrid.py +++ b/cellpack/autopack/BaseGrid.py @@ -35,6 +35,7 @@ ############################################################################### @author: Ludovic Autin, Graham Johnson, & Michel Sanner """ + import logging import numpy from scipy import spatial diff --git a/cellpack/autopack/DBRecipeHandler.py b/cellpack/autopack/DBRecipeHandler.py index 27c35c392..944733c2d 100644 --- a/cellpack/autopack/DBRecipeHandler.py +++ b/cellpack/autopack/DBRecipeHandler.py @@ -1,19 +1,20 @@ import copy import logging import shutil -from datetime import datetime, timezone from enum import Enum from pathlib import Path from cellpack.autopack.interface_objects.database_ids import DATABASE_IDS +from cellpack.autopack.AWSHandler import AWSHandler import hashlib import json -import requests from cellpack.autopack.utils import deep_merge +DB_SETUP_README_URL = "https://github.com/mesoscope/cellpack?tab=readme-ov-file#introduction-to-remote-databases" + class DataDoc(object): def __init__( @@ -47,9 +48,43 @@ def is_obj(comp_or_obj): # in resolved DB data, if the top level of a downloaded comp doesn't have the key `name`, it's an obj return not comp_or_obj.get("name") and "object" in comp_or_obj + @staticmethod + def _is_positional(item): + if isinstance(item, bool): + return False + if isinstance(item, (int, float)): + return True + if isinstance(item, list): + return all(DataDoc._is_positional(x) for x in item) + return False + + @staticmethod + def _normalize_for_hashing(data): + """ + Recursively normalize the input json data so that dedup hashes are + stable across semantically equivalent inputs. + + Categories (see `cellpack/tests/test_data_doc.py` for worked shapes): + - dict key order — sorted by `json.dumps(sort_keys=True)` + - string lists (e.g. region composition refs) — sorted + - mixed string + inline-dict lists — sorted + - pure-dict lists (partners, inline composition entries) — sorted + - positional numeric lists (vectors, colors) — leave as is + - positional nested-numeric lists (bounding boxes) — leave as is + """ + if isinstance(data, dict): + return {k: DataDoc._normalize_for_hashing(v) for k, v in data.items()} + if isinstance(data, list): + normalized = [DataDoc._normalize_for_hashing(item) for item in data] + if all(DataDoc._is_positional(item) for item in normalized): + return normalized + return sorted(normalized, key=lambda x: json.dumps(x, sort_keys=True)) + return data + @staticmethod def generate_hash(doc_data): - doc_str = json.dumps(doc_data, sort_keys=True) + normalized_data = DataDoc._normalize_for_hashing(doc_data) + doc_str = json.dumps(normalized_data, sort_keys=True) return hashlib.sha256(doc_str.encode()).hexdigest() @@ -321,36 +356,6 @@ def __init__(self, settings): self.settings = settings -class ResultDoc: - def __init__(self, db): - self.db = db - - def handle_expired_results(self): - """ - Check if the results in the database are expired and delete them if the linked object expired. - """ - current_utc = datetime.now(timezone.utc) - results = self.db.get_all_docs("results") - if results: - for result in results: - result_data = self.db.doc_to_dict(result) - result_age = current_utc - result_data["timestamp"] - if result_age.days > 180 and not self.validate_existence( - result_data["url"] - ): - self.db.delete_doc("results", self.db.doc_id(result)) - logging.info("Results cleanup complete.") - else: - logging.info("No results found in the database.") - - def validate_existence(self, url): - """ - Validate the existence of an S3 object by checking if the URL is accessible. - Returns True if the URL is accessible. - """ - return requests.head(url).status_code == requests.codes.ok - - class DBUploader(object): """ Handles the uploading of data to the database. @@ -515,6 +520,7 @@ def upload_recipe(self, recipe_meta_data, recipe_data): recipe_to_save = self.upload_collections(recipe_meta_data, recipe_data) recipe_to_save["recipe_path"] = self.db.create_path("recipes", recipe_id) self.upload_data("recipes", recipe_to_save, recipe_id) + return recipe_id def upload_config(self, config_data, source_path): """ @@ -526,51 +532,63 @@ def upload_config(self, config_data, source_path): # update the config data with the firebase doc path config_data["config_path"] = doc_path self.db.update_doc("configs", id, config_data) - return - - def upload_result_metadata(self, file_name, url, job_id=None): - """ - Upload the metadata of the result file to the database. - """ - if self.db: - username = self.db.get_username() - timestamp = self.db.create_timestamp() - self.db.update_or_create( - "results", - file_name, - { - "user": username, - "timestamp": timestamp, - "url": url, - "batch_job_id": job_id, - }, - ) - if job_id: - self.upload_job_status(job_id, "DONE", result_path=url) + return id - def upload_job_status(self, job_id, status, result_path=None, error_message=None): + def upload_job_status( + self, + dedup_hash, + status, + result_path=None, + error_message=None, + outputs_directory=None, + ): """ - Update status for a given job ID + Update status for a given dedup_hash """ if self.db: - timestamp = self.db.create_timestamp() - self.db.update_or_create( - "job_status", - job_id, - { - "timestamp": timestamp, - "status": str(status), - "result_path": result_path, - "error_message": error_message, - }, - ) - - def upload_packing_results_workflow(self, source_folder, recipe_name, job_id): + db_handler = self.db + # If db is AWSHandler, switch to firebase handler for job status updates + if isinstance(self.db, AWSHandler): + handler = DATABASE_IDS.handlers().get(DATABASE_IDS.FIREBASE) + db_handler = handler(default_db="staging") + timestamp = db_handler.create_timestamp() + data = { + "timestamp": timestamp, + "status": str(status), + "error_message": error_message, + } + if result_path: + data["result_path"] = result_path + if outputs_directory: + data["outputs_directory"] = outputs_directory + db_handler.update_or_create("job_status", dedup_hash, data) + + def save_recipe_and_config_to_output(self, output_folder, config_data, recipe_data): + output_path = Path(output_folder) + + recipe_output_path = output_path / "recipe.json" + with open(recipe_output_path, "w") as f: + json.dump(recipe_data, f, indent=2) + logging.debug(f"Saved recipe to {recipe_output_path}") + + config_path = output_path / "config.json" + with open(config_path, "w") as f: + json.dump(config_data, f, indent=2) + logging.debug(f"Saved config to {config_path}") + + def upload_packing_results_workflow( + self, + source_folder, + recipe_name, + dedup_hash, + config_data, + recipe_data, + ): """ Complete packing results upload workflow including folder preparation and s3 upload """ try: - if job_id: + if dedup_hash: source_path = Path(source_folder) if not source_path.exists(): @@ -580,19 +598,24 @@ def upload_packing_results_workflow(self, source_folder, recipe_name, job_id): # prepare unique S3 upload folder parent_folder = source_path.parent - unique_folder_name = f"{source_path.name}_run_{job_id}" + unique_folder_name = f"{source_path.name}_run_{dedup_hash}" s3_upload_folder = parent_folder / unique_folder_name logging.debug(f"outputs will be copied to: {s3_upload_folder}") - # copy outputs to unique upload folder s3_upload_folder.mkdir(parents=True, exist_ok=True) shutil.copytree(source_folder, s3_upload_folder, dirs_exist_ok=True) + if recipe_data and config_data: + self.save_recipe_and_config_to_output( + output_folder=s3_upload_folder, + config_data=config_data, + recipe_data=recipe_data, + ) upload_result = self.upload_outputs_to_s3( output_folder=s3_upload_folder, recipe_name=recipe_name, - job_id=job_id, + dedup_hash=dedup_hash, ) # clean up temporary folder after upload @@ -602,9 +625,12 @@ def upload_packing_results_workflow(self, source_folder, recipe_name, job_id): f"Cleaned up temporary upload folder: {s3_upload_folder}" ) - # update outputs directory in firebase - self.update_outputs_directory( - job_id, upload_result.get("outputs_directory") + # update outputs directory in job status + self.upload_job_status( + dedup_hash, + "DONE", + result_path=upload_result.get("simularium_url"), + outputs_directory=upload_result.get("outputs_directory"), ) return upload_result @@ -613,7 +639,7 @@ def upload_packing_results_workflow(self, source_folder, recipe_name, job_id): logging.error(e) return {"success": False, "error": e} - def upload_outputs_to_s3(self, output_folder, recipe_name, job_id): + def upload_outputs_to_s3(self, output_folder, recipe_name, dedup_hash): """ Upload packing outputs to S3 bucket """ @@ -621,7 +647,7 @@ def upload_outputs_to_s3(self, output_folder, recipe_name, job_id): bucket_name = self.db.bucket_name region_name = self.db.region_name sub_folder_name = self.db.sub_folder_name - s3_prefix = f"{sub_folder_name}/{recipe_name}/{job_id}" + s3_prefix = f"{sub_folder_name}/{recipe_name}/{dedup_hash}" try: upload_result = self.db.upload_directory( @@ -635,8 +661,11 @@ def upload_outputs_to_s3(self, output_folder, recipe_name, job_id): f"{base_url}/{file_info['s3_key']}" for file_info in upload_result["uploaded_files"] ] + simularium_url = None + for url in public_urls: + if url.endswith(".simularium"): + simularium_url = url outputs_directory = f"https://us-west-2.console.aws.amazon.com/s3/buckets/{bucket_name}/{s3_prefix}/" - logging.info( f"Successfully uploaded {upload_result['total_files']} files to {outputs_directory}" ) @@ -645,7 +674,7 @@ def upload_outputs_to_s3(self, output_folder, recipe_name, job_id): return { "success": True, - "run_id": job_id, + "dedup_hash": dedup_hash, "s3_bucket": bucket_name, "s3_prefix": s3_prefix, "public_url_base": f"{base_url}/{s3_prefix}/", @@ -654,30 +683,12 @@ def upload_outputs_to_s3(self, output_folder, recipe_name, job_id): "total_size": upload_result["total_size"], "urls": public_urls, "outputs_directory": outputs_directory, + "simularium_url": simularium_url, } except Exception as e: logging.error(e) return {"success": False, "error": e} - def update_outputs_directory(self, job_id, outputs_directory): - if not self.db or self.db.s3_client: - # switch to firebase handler to update job status - handler = DATABASE_IDS.handlers().get("firebase") - initialized_db = handler(default_db="staging") - if job_id: - timestamp = initialized_db.create_timestamp() - initialized_db.update_or_create( - "job_status", - job_id, - { - "timestamp": timestamp, - "outputs_directory": outputs_directory, - }, - ) - logging.debug( - f"Updated outputs s3 location {outputs_directory} for job ID: {job_id}" - ) - class DBRecipeLoader(object): """ @@ -855,30 +866,10 @@ def compile_db_recipe_data(db_recipe_data, obj_dict, grad_dict, comp_dict): recipe_data["grid_file_path"] = db_recipe_data.get("grid_file_path") if db_recipe_data.get("randomness_seed"): recipe_data["randomness_seed"] = db_recipe_data.get("randomness_seed") + if db_recipe_data.get("description"): + recipe_data["description"] = db_recipe_data.get("description") if grad_dict: recipe_data["gradients"] = [ {**v} for v in DBRecipeLoader.remove_dedup_hash(grad_dict).values() ] return recipe_data - - -class DBMaintenance(object): - """ - Handles the maintenance of the database. - """ - - def __init__(self, db_handler): - self.db = db_handler - self.result_doc = ResultDoc(self.db) - - def cleanup_results(self): - """ - Check if the results in the database are expired and delete them if the linked object expired. - """ - self.result_doc.handle_expired_results() - - def readme_url(self): - """ - Return the URL to the README file for the database setup section. - """ - return "https://github.com/mesoscope/cellpack?tab=readme-ov-file#introduction-to-remote-databases" diff --git a/cellpack/autopack/Environment.py b/cellpack/autopack/Environment.py index 4e6f42eba..9042fab15 100644 --- a/cellpack/autopack/Environment.py +++ b/cellpack/autopack/Environment.py @@ -124,6 +124,7 @@ def __init__(self, config=None, recipe=None): self.config_data = config self.recipe_data = recipe + self.dedup_hash = None name = recipe["name"] self.log = logging.getLogger("env") self.log.propagate = False diff --git a/cellpack/autopack/FirebaseHandler.py b/cellpack/autopack/FirebaseHandler.py index 3c21be4b4..4364ba9fc 100644 --- a/cellpack/autopack/FirebaseHandler.py +++ b/cellpack/autopack/FirebaseHandler.py @@ -45,6 +45,10 @@ def which_db(default_db=None): if default_db in options.values(): log.debug(f"Using {default_db} database -------------") return default_db + # detect if running in a non-interactive environment(CI, Docker, etc), default to staging db + if not os.isatty(0): + log.debug("Non-interactive environment detected, using staging database") + return "staging" choice = input( f"Enter number for database ({', '.join([f'{k}: {v}' for k, v in options.items()])}): " ).strip() diff --git a/cellpack/autopack/GeometryTools.py b/cellpack/autopack/GeometryTools.py index 08275b99c..1b6181ba5 100644 --- a/cellpack/autopack/GeometryTools.py +++ b/cellpack/autopack/GeometryTools.py @@ -13,6 +13,7 @@ http://crowsandcats.blogspot.com/2013/04/cube-sphere-intersection-volume.html Copyright © Andrew White """ + import math import numpy as np diff --git a/cellpack/autopack/IOutils.py b/cellpack/autopack/IOutils.py index 519f7c736..208ca4689 100644 --- a/cellpack/autopack/IOutils.py +++ b/cellpack/autopack/IOutils.py @@ -4,6 +4,7 @@ @author: Ludovic Autin """ + import json import os import pickle diff --git a/cellpack/autopack/MeshStore.py b/cellpack/autopack/MeshStore.py index 97d1c53cd..53d060ec9 100644 --- a/cellpack/autopack/MeshStore.py +++ b/cellpack/autopack/MeshStore.py @@ -281,7 +281,7 @@ def get_smallest_radius(self, geomname, center): mesh = self.get_object(geomname) if mesh is not None: query = trimesh.proximity.ProximityQuery(mesh) - (_, distance, _) = query.on_surface([center]) + _, distance, _ = query.on_surface([center]) return distance[0] return 1.0 @@ -289,7 +289,7 @@ def get_normal(self, geomname, point_pos): mesh = self.get_object(geomname) if mesh is not None: query = trimesh.proximity.ProximityQuery(mesh) - (distance, triangle_ids) = query.vertex([point_pos]) + distance, triangle_ids = query.vertex([point_pos]) triangle_id = triangle_ids[0] return mesh.vertex_normals[triangle_id] diff --git a/cellpack/autopack/Serializable.py b/cellpack/autopack/Serializable.py index 52ef6b97a..e29dd4949 100644 --- a/cellpack/autopack/Serializable.py +++ b/cellpack/autopack/Serializable.py @@ -4,10 +4,10 @@ @author: ludo """ + # serializabl;e class for auopack recipe import json - # toDO class Assambly for nesting of protein quaternary structure. # class sAssambly # static_id=0 diff --git a/cellpack/autopack/__init__.py b/cellpack/autopack/__init__.py index 77ddaf465..e9317240b 100755 --- a/cellpack/autopack/__init__.py +++ b/cellpack/autopack/__init__.py @@ -34,6 +34,7 @@ AF @author: Ludovic Autin with editing by Graham Johnson """ + import getpass import json import logging @@ -205,6 +206,7 @@ def load_path_preferences(): "autopackdata": appdata, f"{DATABASE_IDS.GITHUB.value}:": autoPACKserver, f"{DATABASE_IDS.FIREBASE.value}:": None, + f"{DATABASE_IDS.AWS.value}:": None, } @@ -426,7 +428,7 @@ def load_file( if not initialize_db._initialized: readme_url = "https://github.com/mesoscope/cellpack?tab=readme-ov-file#introduction-to-remote-databases" sys.exit( - f"The selected database: {database_name} is not initialized. Please set up credentials to pack remote recipes. Refer to the instructions at {readme_url}" + f"The selected database: {database_name} is not initialized. Please set up credentials to pack remote recipes. Refer to the instructions at {readme_url}, or try cellPACK web interface: https://cellpack.allencell.org (no setup required)" ) db_handler = DBRecipeLoader(initialize_db) db_handler.validate_input_recipe_path(filename) diff --git a/cellpack/autopack/ingredient/Ingredient.py b/cellpack/autopack/ingredient/Ingredient.py index b4771da6e..e8a374305 100644 --- a/cellpack/autopack/ingredient/Ingredient.py +++ b/cellpack/autopack/ingredient/Ingredient.py @@ -1620,10 +1620,10 @@ def attempt_to_pack_at_grid_location( # TODO: make this work for ingredients other than single spheres success = True - (jtrans, rotMatj) = self.get_new_jitter_location_and_rotation( + jtrans, rotMatj = self.get_new_jitter_location_and_rotation( env, target_grid_point_position, rotation_matrix ) - (insidePoints, newDistPoints) = self.pack_at_grid_pt_location( + insidePoints, newDistPoints = self.pack_at_grid_pt_location( env, jtrans, rotMatj, diff --git a/cellpack/autopack/interface_objects/__init__.py b/cellpack/autopack/interface_objects/__init__.py index 0bf352e24..55a0ec27f 100644 --- a/cellpack/autopack/interface_objects/__init__.py +++ b/cellpack/autopack/interface_objects/__init__.py @@ -1,5 +1,6 @@ # -*- coding: utf-8 -*- """Interface classes for cellpack. These are to establish data structures.""" + from .default_values import ( # noqa: F401 default_recipe_values, DEFAULT_GRADIENT_MODE_SETTINGS, diff --git a/cellpack/autopack/interface_objects/database_ids.py b/cellpack/autopack/interface_objects/database_ids.py index 7ef4203a4..18469166d 100644 --- a/cellpack/autopack/interface_objects/database_ids.py +++ b/cellpack/autopack/interface_objects/database_ids.py @@ -14,7 +14,9 @@ def with_colon(cls): @classmethod def handlers(cls): - def create_aws_handler(bucket_name, sub_folder_name, region_name): + def create_aws_handler( + bucket_name=None, sub_folder_name=None, region_name=None + ): return AWSHandler( bucket_name=bucket_name, sub_folder_name=sub_folder_name, diff --git a/cellpack/autopack/interface_objects/default_values.py b/cellpack/autopack/interface_objects/default_values.py index 199b65f18..06988f595 100644 --- a/cellpack/autopack/interface_objects/default_values.py +++ b/cellpack/autopack/interface_objects/default_values.py @@ -19,7 +19,6 @@ "objects", "gradients", "recipes", - "results", "configs", "recipes_edited", ] diff --git a/cellpack/autopack/loaders/config_loader.py b/cellpack/autopack/loaders/config_loader.py index 7e298c3e4..e64ae6ae1 100644 --- a/cellpack/autopack/loaders/config_loader.py +++ b/cellpack/autopack/loaders/config_loader.py @@ -1,5 +1,7 @@ # -*- coding: utf-8 -*- import json +import logging +import multiprocessing import os from json import encoder @@ -97,6 +99,32 @@ def _test_types(config): f"number_of_processes must be an integer >= 1, not {config['number_of_processes']}" ) + @staticmethod + def _migrate_legacy_keys(config): + """ + Map deprecated config keys onto their current equivalents so that older + config files keep working. Currently handles the legacy ``parallel`` + boolean, which was renamed to ``number_of_processes`` (an integer >= 1). + """ + if "parallel" in config: + legacy_parallel = config.pop("parallel") + # Only honor the legacy value if number_of_processes wasn't set explicitly. + if "number_of_processes" not in config: + if legacy_parallel: + config["number_of_processes"] = max( + 1, int(0.8 * multiprocessing.cpu_count()) + ) + else: + config["number_of_processes"] = 1 + logging.warning( + "Config key 'parallel' is deprecated; use 'number_of_processes' " + "(integer >= 1) instead. Interpreting parallel=%s as " + "number_of_processes=%s.", + legacy_parallel, + config.get("number_of_processes", 1), + ) + return config + @staticmethod def _migrate_version(config): return config @@ -114,8 +142,10 @@ def _read(self, use_docker=False): initialize_db = db(default_db="staging") if use_docker else db() db_handler = DBRecipeLoader(initialize_db) config = db_handler.read_config(self.file_path) + config = ConfigLoader._migrate_legacy_keys(config) else: new_values = json.load(open(self.file_path, "r")) + new_values = ConfigLoader._migrate_legacy_keys(new_values) config = ConfigLoader.default_values.copy() config.update(new_values) if config["version"] != self.latest_version: diff --git a/cellpack/autopack/loaders/migrate_v1_to_v2.py b/cellpack/autopack/loaders/migrate_v1_to_v2.py index 5155ae421..919d8e72f 100644 --- a/cellpack/autopack/loaders/migrate_v1_to_v2.py +++ b/cellpack/autopack/loaders/migrate_v1_to_v2.py @@ -63,6 +63,14 @@ def get_representations(old_ingredient): return representations +def normalize_color(color): + if color is None: + return color + if any(component > 1 for component in color): + return [component / 255 for component in color] + return color + + def constrain_angle(angle): if -pi <= angle <= pi: return angle @@ -85,6 +93,8 @@ def migrate_ingredient(old_ingredient): if attribute in v1_to_v2_name_map: if attribute == "Type": value = ingredient_types_map[old_ingredient[attribute]] + elif attribute == "color": + value = normalize_color(old_ingredient[attribute]) else: value = old_ingredient[attribute] new_ingredient[v1_to_v2_name_map[attribute]] = value diff --git a/cellpack/autopack/loaders/recipe_loader.py b/cellpack/autopack/loaders/recipe_loader.py index cd06fca2d..6d6676fb3 100644 --- a/cellpack/autopack/loaders/recipe_loader.py +++ b/cellpack/autopack/loaders/recipe_loader.py @@ -9,7 +9,7 @@ from cellpack.autopack.DBRecipeHandler import DBRecipeLoader from cellpack.autopack.interface_objects import ( - GradientData, + DEFAULT_GRADIENT_MODE_SETTINGS, Representations, default_recipe_values, ) @@ -31,22 +31,29 @@ class RecipeLoader(object): # TODO: add all default values here default_values = default_recipe_values.copy() - def __init__(self, input_file_path, save_converted_recipe=False, use_docker=False): - _, file_extension = os.path.splitext(input_file_path) + def __init__( + self, + input_data, + save_converted_recipe=False, + use_docker=False, + ): self.current_version = CURRENT_VERSION - self.file_path = input_file_path - self.file_extension = file_extension self.ingredient_list = [] self.compartment_list = [] self.save_converted_recipe = save_converted_recipe - # set CURRENT_RECIPE_PATH appropriately for remote(firebase) vs local recipes - if autopack.is_remote_path(self.file_path): - autopack.CURRENT_RECIPE_PATH = os.path.join( - os.getcwd(), "examples", "recipes", "v2" - ) + if isinstance(input_data, dict): + self._json_recipe = input_data + self.file_path = None else: - autopack.CURRENT_RECIPE_PATH = os.path.dirname(self.file_path) + self.file_path = input_data + self._json_recipe = None + if autopack.is_remote_path(self.file_path): + autopack.CURRENT_RECIPE_PATH = os.path.join( + os.getcwd(), "examples", "recipes", "v2" + ) + else: + autopack.CURRENT_RECIPE_PATH = os.path.dirname(self.file_path) self.recipe_data = self._read(use_docker=use_docker) @@ -144,6 +151,33 @@ def _sanitize_format_version(recipe_data): format_version = recipe_data["format_version"] return format_version + @staticmethod + def _normalize_gradients(gradients): + """ + Normalize gradients to the list-of-dicts format and fill in + default settings for any missing keys. + """ + if not gradients: + return gradients + + # firebase recipes already store gradients as a list of dicts; + # file recipes store them as a dict keyed by gradient name + if isinstance(gradients, dict): + gradient_items = [ + {**gradient_dict, "name": gradient_name} + for gradient_name, gradient_dict in gradients.items() + ] + else: + gradient_items = gradients + + normalized = [] + for gradient in gradient_items: + # fill any missing top-level keys from the defaults without + # overwriting values the recipe set + filled = {**copy.deepcopy(DEFAULT_GRADIENT_MODE_SETTINGS), **gradient} + normalized.append(filled) + return normalized + def _migrate_version(self, old_recipe): converted = False if old_recipe["format_version"] == "1.0": @@ -169,16 +203,25 @@ def _migrate_version(self, old_recipe): ) def _read(self, resolve_inheritance=True, use_docker=False): - new_values, database_name, is_unnested_firebase = autopack.load_file( - self.file_path, cache="recipes", use_docker=use_docker - ) + database_name = None + is_unnested_firebase = False + new_values = self._json_recipe + if new_values is None: + # Read recipe from filepath + new_values, database_name, is_unnested_firebase = autopack.load_file( + self.file_path, cache="recipes", use_docker=use_docker + ) + + if "composition" in new_values: + new_values["composition"] = DBRecipeLoader.remove_empty( + new_values["composition"] + ) + if database_name == "firebase": if is_unnested_firebase: objects = new_values.get("objects", {}) gradients = new_values.get("gradients", {}) - composition = DBRecipeLoader.remove_empty( - new_values.get("composition", {}) - ) + composition = new_values.get("composition", {}) else: objects, gradients, composition = DBRecipeLoader.collect_and_sort_data( new_values["composition"] @@ -201,6 +244,11 @@ def _read(self, resolve_inheritance=True, use_docker=False): recipe_data["objects"] = RecipeLoader.resolve_inheritance( recipe_data["objects"] ) + if "gradients" in recipe_data: + recipe_data["gradients"] = RecipeLoader._normalize_gradients( + recipe_data["gradients"] + ) + # validate recipe after migration to v2.1 format but before transforming to class instances try: RecipeValidator.validate_recipe(recipe_data) @@ -209,6 +257,12 @@ def _read(self, resolve_inheritance=True, use_docker=False): formatted_error = RecipeValidator.format_validation_error(e) raise ValueError(f"Recipe validation failed:\n{formatted_error}") + # keep a serializable copy after all dict-level normalization but before + # converting to class instances. this is the human-readable source of + # truth used for UI download / DB upload, and now matches both the packed + # recipe and the database's list-of-dicts gradient format. + self.serializable_recipe_data = copy.deepcopy(recipe_data) + if "objects" in recipe_data: for _, obj in recipe_data["objects"].items(): reps = obj["representations"] if "representations" in obj else {} @@ -231,15 +285,6 @@ def _read(self, resolve_inheritance=True, use_docker=False): if "type" in obj and not INGREDIENT_TYPE.is_member(obj["type"]): raise TypeError(f"{obj['type']} is not an allowed type") - # handle gradients - # gradients in firebase recipes are already stored as a list of dicts - if "gradients" in recipe_data and not isinstance( - recipe_data["gradients"], list - ): - gradients = [] - for gradient_name, gradient_dict in recipe_data["gradients"].items(): - gradients.append(GradientData(gradient_dict, gradient_name).data) - recipe_data["gradients"] = gradients return recipe_data def _load_json(self): diff --git a/cellpack/autopack/transformation.py b/cellpack/autopack/transformation.py index e0b43c0fb..45c24f213 100644 --- a/cellpack/autopack/transformation.py +++ b/cellpack/autopack/transformation.py @@ -185,6 +185,7 @@ True """ + from __future__ import division, print_function diff --git a/cellpack/autopack/upy/hostHelper.py b/cellpack/autopack/upy/hostHelper.py index 2585e723a..ed954524f 100644 --- a/cellpack/autopack/upy/hostHelper.py +++ b/cellpack/autopack/upy/hostHelper.py @@ -16,6 +16,7 @@ You should have received a copy of the GNU General Public License along with upy. If not, see . """ + import math import os import random diff --git a/cellpack/autopack/upy/simularium/simularium_helper.py b/cellpack/autopack/upy/simularium/simularium_helper.py index 8801489bc..87c616e18 100644 --- a/cellpack/autopack/upy/simularium/simularium_helper.py +++ b/cellpack/autopack/upy/simularium/simularium_helper.py @@ -1,5 +1,6 @@ # -*- coding: utf-8 -*- # standardmodule +import logging import os import webbrowser from pathlib import Path @@ -21,7 +22,7 @@ from simulariumio.cellpack import HAND_TYPE, CellpackConverter from simulariumio.constants import DISPLAY_TYPE, VIZ_TYPE -from cellpack.autopack.DBRecipeHandler import DBMaintenance, DBUploader +from cellpack.autopack.DBRecipeHandler import DB_SETUP_README_URL from cellpack.autopack.interface_objects.database_ids import DATABASE_IDS from cellpack.autopack.upy import hostHelper from cellpack.autopack.upy.simularium.plots import PlotData @@ -1330,7 +1331,9 @@ def writeToFile(self, file_name, bb, recipe_name, version): n_subpoints[t][n] = 0 n += 1 - camera_z_position = box_size[2] if box_size[2] > 10 else 100.0 + # use max dimension to make sure camera captures entire scene + max_box_dimension = max(box_size) + camera_z_position = max_box_dimension * 2.5 converted_data = TrajectoryData( meta_data=MetaData( box_size=np.array(box_size), @@ -1382,62 +1385,29 @@ def raycast(self, **kw): def raycast_test(self, obj, start, end, length, **kw): return - def post_and_open_file(self, file_name, open_results_in_browser=True): + def post_and_open_file(self, file_name, open_results_in_browser, dedup_hash=None): simularium_file = Path(f"{file_name}.simularium") - url = None - job_id = os.environ.get("AWS_BATCH_JOB_ID", None) - file_name, url = simulariumHelper.store_result_file( - simularium_file, storage="aws", batch_job_id=job_id - ) - if file_name and url: - simulariumHelper.store_metadata( - file_name, url, db="firebase", job_id=job_id - ) - if open_results_in_browser: + if dedup_hash is None: + url = simulariumHelper.store_result_file(simularium_file, storage="aws") + if url and open_results_in_browser: simulariumHelper.open_in_simularium(url) @staticmethod - def store_result_file(file_path, storage=None, batch_job_id=None): + def store_result_file(file_path, storage=None, sub_folder="simularium"): if storage == "aws": handler = DATABASE_IDS.handlers().get(storage) - # if batch_job_id is not None, then we are in a batch job and should use the temp bucket - # TODO: use cellpack-results bucket for batch jobs once we have the correct permissions - if batch_job_id: - initialized_handler = handler( - bucket_name="cellpack-demo", - sub_folder_name="simularium", - region_name="us-west-2", - ) - else: - initialized_handler = handler( - bucket_name="cellpack-results", - sub_folder_name="simularium", - region_name="us-west-2", - ) - file_name, url = initialized_handler.save_file_and_get_url(file_path) - if not file_name or not url: - db_maintainer = DBMaintenance(initialized_handler) - print( - f"If AWS access needed, please refer to the instructions at {db_maintainer.readme_url()}. \nSkipping the opening of new browser tabs -------------" - ) - return file_name, url - - @staticmethod - def store_metadata(file_name, url, db=None, job_id=None): - if db == "firebase": - handler = DATABASE_IDS.handlers().get(db) - initialized_db = handler( - default_db="staging" - ) # default to staging for metadata uploads - if initialized_db._initialized: - db_uploader = DBUploader(initialized_db) - db_uploader.upload_result_metadata(file_name, url, job_id) - else: - db_maintainer = DBMaintenance(initialized_db) - print( - f"Firebase credentials are not found. If needed, please refer to the instructions at {db_maintainer.readme_url()}. \nSkipping firebase staging database -------------" + initialized_handler = handler( + bucket_name="cellpack-results", + sub_folder_name=sub_folder, + region_name="us-west-2", + ) + _, url = initialized_handler.save_file_and_get_url(file_path) + if not url: + logging.warning( + f"Skipping browser opening, upload credentials not configured. For setup instructions see: {DB_SETUP_README_URL}" ) - return + return url + return None @staticmethod def open_in_simularium(aws_url): diff --git a/cellpack/autopack/validation/recipe_models.py b/cellpack/autopack/validation/recipe_models.py index ae6fd979e..a64d47c26 100644 --- a/cellpack/autopack/validation/recipe_models.py +++ b/cellpack/autopack/validation/recipe_models.py @@ -224,7 +224,7 @@ class RecipeObject(BaseModel): ] = None weight: Optional[float] = Field(None, ge=0) is_attractor: Optional[bool] = None - priority: Optional[int] = None + priority: Optional[Union[int, float]] = None jitterMax: Optional[ThreeFloatArray] = Field( None, min_length=3, max_length=3, alias="jitterMax" @@ -316,7 +316,7 @@ def validate_partners_format(cls, v): class CompositionItem(BaseModel): object: str count: int = Field(5, ge=0) - priority: Optional[int] = None + priority: Optional[Union[int, float]] = None class CompositionRegions(BaseModel): @@ -329,7 +329,7 @@ class CompositionRegions(BaseModel): class CompositionEntry(BaseModel): object: Optional[str] = None count: Optional[int] = Field(None, ge=0) - priority: Optional[int] = None + priority: Optional[Union[int, float]] = None regions: Optional[CompositionRegions] = None @model_validator(mode="after") @@ -343,10 +343,12 @@ def validate_entry_content(self): # RECIPE-METADATA-LEVEL class Recipe(BaseModel): name: str + description: Optional[str] = None version: str = Field("1.0.0") format_version: str = Field("2.0") bounding_box: List[List[float]] = Field([[0, 0, 0], [100, 100, 100]]) grid_file_path: Optional[str] = None + randomness_seed: Optional[int] = None objects: Dict[str, RecipeObject] = Field(default_factory=dict) gradients: Union[Dict[str, RecipeGradient], List[Dict[str, Any]]] = Field( default_factory=dict @@ -491,20 +493,6 @@ def validate_gradient_surface_objects(self): ) return self - @model_validator(mode="after") - def validate_gradient_combinations(self): - """Validate gradient combinations in object gradient lists""" - if hasattr(self, "objects") and self.objects: - for obj_name, obj_data in self.objects.items(): - if hasattr(obj_data, "gradient") and obj_data.gradient is not None: - if isinstance(obj_data.gradient, list): - # multiple gradients - validate combination - if len(obj_data.gradient) < 2: - raise ValueError( - f"objects.{obj_name}.gradient: gradient lists must contain at least 2 gradients" - ) - return self - @model_validator(mode="after") def validate_object_inheritance(self): """Validate that object inherit references point to existing objects in the objects section""" diff --git a/cellpack/autopack/writers/__init__.py b/cellpack/autopack/writers/__init__.py index 4b6ce2f7f..0985cbbe5 100644 --- a/cellpack/autopack/writers/__init__.py +++ b/cellpack/autopack/writers/__init__.py @@ -2,7 +2,6 @@ """Write out data for cellpack.""" - import json import os from collections import OrderedDict @@ -201,12 +200,13 @@ def save_as_simularium(self, env, seed_to_results_map): env.version, ) number_of_packings = env.config_data.get("number_of_packings", 1) + open_results_in_browser = env.config_data.get("open_results_in_browser", True) upload_results = env.config_data.get("upload_results", True) - if upload_results and (number_of_packings == 1 or is_aggregate): - open_results_in_browser = env.config_data.get( - "open_results_in_browser", True + dedup_hash = getattr(env, "dedup_hash") + if (number_of_packings == 1 or is_aggregate) and upload_results: + autopack.helper.post_and_open_file( + file_name, open_results_in_browser, dedup_hash ) - autopack.helper.post_and_open_file(file_name, open_results_in_browser) def save_Mixed_asJson( self, diff --git a/cellpack/bin/cleanup_tasks.py b/cellpack/bin/cleanup_tasks.py deleted file mode 100644 index 08217aa04..000000000 --- a/cellpack/bin/cleanup_tasks.py +++ /dev/null @@ -1,20 +0,0 @@ -from cellpack.autopack.DBRecipeHandler import DBMaintenance -from cellpack.autopack.interface_objects.database_ids import DATABASE_IDS - - -def run_cleanup(db_id=DATABASE_IDS.FIREBASE): - """ - Performs cleanup operations on expired database entries. - This function is executed as part of a scheduled task defined in .github/workflows/cleanup-firebase.yml - - Args: - db_id(str): The database id to use - """ - handler = DATABASE_IDS.handlers().get(db_id) - initialized_db = handler(default_db="staging") - db_maintainer = DBMaintenance(initialized_db) - db_maintainer.cleanup_results() - - -if __name__ == "__main__": - run_cleanup() diff --git a/cellpack/bin/pack.py b/cellpack/bin/pack.py index 4b4a23bba..0d4cfede0 100644 --- a/cellpack/bin/pack.py +++ b/cellpack/bin/pack.py @@ -1,6 +1,5 @@ import logging import logging.config -import os import time from pathlib import Path @@ -25,23 +24,28 @@ def pack( - recipe, config_path=None, analysis_config_path=None, docker=False, validate=True + recipe, + config_path=None, + analysis_config_path=None, + docker=False, + hash=None, ): """ Initializes an autopack packing from the command line - :param recipe: string argument, path to recipe + :param recipe: string argument, path to recipe file, or a dictionary representing a recipe :param config_path: string argument, path to packing config file :param analysis_config_path: string argument, path to analysis config file :param docker: boolean argument, are we using docker - :param validate: boolean argument, validate recipe before packing + :param hash: string argument, dedup hash identifier for tracking/caching results :return: void """ packing_config_data = ConfigLoader(config_path, docker).config - recipe_data = RecipeLoader( + recipe_loader = RecipeLoader( recipe, packing_config_data["save_converted_recipe"], docker - ).recipe_data + ) + recipe_data = recipe_loader.recipe_data analysis_config_data = {} if analysis_config_path is not None: analysis_config_data = AnalysisConfigLoader(analysis_config_path).config @@ -51,7 +55,9 @@ def pack( autopack.helper = helper env = Environment(config=packing_config_data, recipe=recipe_data) env.helper = helper + env.dedup_hash = hash + log.debug("Using cellpack package from: %s", str(Path(autopack.__file__).parent.parent)) log.info("Packing recipe: %s", recipe_data["name"]) log.info("Outputs will be saved to %s", env.out_folder) @@ -77,22 +83,23 @@ def pack( env.buildGrid(rebuild=True) env.pack_grid(verbose=0, usePP=False) - if docker: - job_id = os.environ.get("AWS_BATCH_JOB_ID", None) - if job_id: - handler = DATABASE_IDS.handlers().get(DATABASE_IDS.AWS) - # temporarily using demo bucket before permissions are granted - initialized_handler = handler( - bucket_name="cellpack-demo", - sub_folder_name="runs", - region_name="us-west-2", - ) - uploader = DBUploader(db_handler=initialized_handler) - uploader.upload_packing_results_workflow( - source_folder=env.out_folder, - recipe_name=recipe_data["name"], - job_id=job_id, - ) + # Upload results to S3 for server-initiated packings (docker and hash are both provided) + if docker and hash: + handler = DATABASE_IDS.handlers().get(DATABASE_IDS.AWS) + # temporarily using demo bucket before permissions are granted + initialized_handler = handler( + bucket_name="cellpack-demo", + sub_folder_name="runs", + region_name="us-west-2", + ) + uploader = DBUploader(db_handler=initialized_handler) + uploader.upload_packing_results_workflow( + source_folder=env.out_folder, + recipe_name=recipe_data["name"], + dedup_hash=hash, + config_data=packing_config_data, + recipe_data=recipe_loader.serializable_recipe_data, + ) def main(): diff --git a/cellpack/bin/simularium_converter.py b/cellpack/bin/simularium_converter.py index abe2c9726..53261ae5d 100644 --- a/cellpack/bin/simularium_converter.py +++ b/cellpack/bin/simularium_converter.py @@ -390,7 +390,7 @@ def main(): converter.fill_in_empty_fiber_data(time_point_index) if converter.debug: print("SUBPOINTS LENGTH", len(converter.subpoints[time_point_index])) - camera_z_position = box_size[2] if box_size[2] > 10 else 100.0 + camera_z_position = box_size[2] * 1.5 converted_data = TrajectoryData( meta_data=MetaData( box_size=np.array(box_size), diff --git a/cellpack/bin/upload.py b/cellpack/bin/upload.py index 8a7616ce5..59fc2104e 100644 --- a/cellpack/bin/upload.py +++ b/cellpack/bin/upload.py @@ -1,9 +1,10 @@ import sys import fire +import json from cellpack.autopack.FirebaseHandler import FirebaseHandler -from cellpack.autopack.DBRecipeHandler import DBUploader, DBMaintenance - +from cellpack.autopack.DBRecipeHandler import DBUploader, DB_SETUP_README_URL +from cellpack.autopack.upy.simularium.simularium_helper import simulariumHelper from cellpack.autopack.interface_objects.database_ids import DATABASE_IDS from cellpack.autopack.loaders.config_loader import ConfigLoader from cellpack.autopack.loaders.recipe_loader import RecipeLoader @@ -21,6 +22,8 @@ def get_recipe_metadata(loader): "bounding_box": loader.recipe_data["bounding_box"], "composition": {}, } + if "description" in loader.recipe_data: + recipe_meta_data["description"] = loader.recipe_data["description"] if "grid_file_path" in loader.recipe_data: recipe_meta_data["grid_file_path"] = loader.recipe_data["grid_file_path"] if "randomness_seed" in loader.recipe_data: @@ -34,12 +37,40 @@ def upload( recipe_path=None, config_path=None, db_id=DATABASE_IDS.FIREBASE, + studio: bool = False, + fields: str = None, + name: str = None, + output_file: str = None, ): """ Uploads a recipe to the database + :param recipe: string argument + path to local recipe file to upload to firebase + :param config: string argument + path to local config file to upload to firebase + :param db_id: string argument + database ID to use for the upload + :param studio: boolean argument + upload for use in cellPACK studio if True + :param fields: string argument + path to local editable fields file to upload to firebase + :param name: string argument + display name for recipe in studio selection menu + :param output_file: string argument + path to local simularium output file to upload + :return: void """ + if studio and (not name or not recipe_path or not fields): + sys.exit( + "To upload a recipe for cellPACK studio, please provide --name, --recipe_path, and --fields arguments." + ) + + recipe_id = "" + config_id = "" + result_url = "" + editable_fields_ids = [] if db_id == DATABASE_IDS.FIREBASE: # fetch the service key json file db_handler = FirebaseHandler() @@ -49,15 +80,33 @@ def upload( recipe_loader = RecipeLoader(recipe_path) recipe_full_data = recipe_loader._read(resolve_inheritance=False) recipe_meta_data = get_recipe_metadata(recipe_loader) - db_handler.upload_recipe(recipe_meta_data, recipe_full_data) + recipe_id = db_handler.upload_recipe(recipe_meta_data, recipe_full_data) if config_path: config_data = ConfigLoader(config_path).config - db_handler.upload_config(config_data, config_path) + config_id = db_handler.upload_config(config_data, config_path) + if fields: + editable_fields_data = json.load(open(fields, "r")) + for field in editable_fields_data.get("editable_fields", []): + id, _ = db_handler.upload_data("editable_fields", field) + editable_fields_ids.append(id) + if output_file: + result_url = simulariumHelper.store_result_file( + output_file, storage="aws", sub_folder="client" + ) + if studio: + recipe_metadata = { + "name": name, + "recipe": recipe_id, + "config": config_id, + "editable_fields": editable_fields_ids, + "result_path": result_url, + } + # Upload the combined recipe metadata to example_packings collection for studio + db_handler.upload_data("example_packings", recipe_metadata) else: - db_maintainer = DBMaintenance(db_handler) sys.exit( - f"The selected database is not initialized. Please set up Firebase credentials to upload recipes. Refer to the instructions at {db_maintainer.readme_url()} " + f"The selected database is not initialized. Please set up Firebase credentials to upload recipes. Refer to the instructions at {DB_SETUP_README_URL} " ) diff --git a/cellpack/tests/packing-configs/test_gradient_mixing.json b/cellpack/tests/packing-configs/test_gradient_mixing.json new file mode 100644 index 000000000..79203469b --- /dev/null +++ b/cellpack/tests/packing-configs/test_gradient_mixing.json @@ -0,0 +1,21 @@ +{ + "name": "test_gradient_mixing", + "out": "out", + "save_analyze_result": true, + "show_progress_bar": true, + "save_plot_figures": false, + "load_from_grid_file": true, + "spacing": 2, + "image_export_options": { + "hollow": false, + "voxel_size": [ + 1, + 1, + 1 + ], + "projection_axis": "z" + }, + "open_results_in_browser": false, + "upload_results": false, + "number_of_packings": 1 +} \ No newline at end of file diff --git a/cellpack/tests/recipes/v2/test_peroxisome_combined_gradient.json b/cellpack/tests/recipes/v2/test_peroxisome_combined_gradient.json new file mode 100644 index 000000000..b94d79cf8 --- /dev/null +++ b/cellpack/tests/recipes/v2/test_peroxisome_combined_gradient.json @@ -0,0 +1,153 @@ +{ + "version": "interpolated_743916", + "format_version": "2.1", + "name": "peroxisome", + "bounding_box": [ + [ + 35.325, + 35.325, + 7.125 + ], + [ + 210.675, + 210.675, + 106.875 + ] + ], + "objects": { + "membrane_mesh": { + "type": "mesh", + "color": [ + 1, + 0, + 1 + ], + "representations": { + "mesh": { + "path": "s3://cellpack-analysis-data/structure_data/SLC25A17/meshes", + "name": "mem_mesh_743916.obj", + "format": "obj" + } + } + }, + "nucleus_mesh": { + "type": "mesh", + "color": [ + 0, + 1, + 1 + ], + "representations": { + "mesh": { + "path": "s3://cellpack-analysis-data/structure_data/SLC25A17/meshes", + "name": "nuc_mesh_743916.obj", + "format": "obj" + } + } + }, + "peroxisome": { + "jitter_attempts": 300, + "type": "single_sphere", + "color": [ + 0.2, + 0.7, + 0.1 + ], + "radius": 0.2677546285806425, + "packing_mode": "gradient", + "gradient": [ + "uniform", + "nucleus_gradient", + "membrane_gradient", + "apical_gradient" + ], + "gradient_weights": { + "uniform": 0.0, + "nucleus_gradient": 0.3323145062439923, + "membrane_gradient": 0.0, + "apical_gradient": 0.6676854937560077 + } + } + }, + "composition": { + "bounding_area": { + "regions": { + "interior": [ + "membrane" + ] + } + }, + "membrane": { + "object": "membrane_mesh", + "count": 1, + "regions": { + "interior": [ + "nucleus", + { + "object": "peroxisome", + "count": 59 + } + ] + } + }, + "nucleus": { + "object": "nucleus_mesh", + "count": 1, + "regions": { + "interior": [] + } + } + }, + "randomness_seed": 743916, + "grid_file_path": "s3://cellpack-analysis-data/structure_data/SLC25A17/grids/743916_grid.dat", + "gradients": { + "uniform": { + "description": "uniform distribution throughout the cell volume", + "mode": "uniform" + }, + "nucleus_gradient": { + "description": "gradient based on distance from the surface of the nucleus mesh", + "mode": "surface", + "mode_settings": { + "object": "nucleus", + "scale_to_next_surface": false + }, + "weight_mode": "exponential", + "weight_mode_settings": { + "decay_length": 0.1 + } + }, + "membrane_gradient": { + "description": "gradient based on distance from the surface of the membrane mesh", + "mode": "surface", + "mode_settings": { + "object": "membrane", + "scale_to_next_surface": false + }, + "weight_mode": "exponential", + "weight_mode_settings": { + "decay_length": 0.01 + } + }, + "apical_gradient": { + "description": "gradient based on distance from a plane", + "mode": "vector", + "mode_settings": { + "direction": [ + 0, + 0, + 1 + ], + "center": [ + 123.0, + 123.0, + 106.875 + ] + }, + "weight_mode": "exponential", + "weight_mode_settings": { + "decay_length": 0.7 + } + } + } +} \ No newline at end of file diff --git a/cellpack/tests/test_aws_handler.py b/cellpack/tests/test_aws_handler.py index e1514e993..ed3d0f37b 100644 --- a/cellpack/tests/test_aws_handler.py +++ b/cellpack/tests/test_aws_handler.py @@ -31,7 +31,7 @@ def test_get_aws_object_key(): assert object_key == "test_folder/test_file" -def test_upload_file(): +def test_upload_file(tmp_path): with mock_aws(): aws_handler = AWSHandler( bucket_name="test_bucket", @@ -43,13 +43,13 @@ def test_upload_file(): Bucket="test_bucket", CreateBucketConfiguration={"LocationConstraint": "us-west-2"}, ) - with open("test_file.txt", "w") as file: - file.write("test file") - file_name = aws_handler.upload_file("test_file.txt") + test_file = tmp_path / "test_file.txt" + test_file.write_text("test file") + file_name = aws_handler.upload_file(str(test_file)) assert file_name == "test_folder/test_file.txt" -def test_create_presigned_url(): +def test_create_presigned_url(tmp_path): with mock_aws(), patch.object(AWSHandler, "_s3_client") as mock_client: presigned_url = "https://s3.us-west-2.amazonaws.com/test_bucket/test_folder/test_file.txt?query=string" mock_client.generate_presigned_url.return_value = presigned_url @@ -63,9 +63,9 @@ def test_create_presigned_url(): Bucket="test_bucket", CreateBucketConfiguration={"LocationConstraint": "us-west-2"}, ) - with open("test_file.txt", "w") as file: - file.write("test file") - aws_handler.upload_file("test_file.txt") + test_file = tmp_path / "test_file.txt" + test_file.write_text("test file") + aws_handler.upload_file(str(test_file)) url = aws_handler.create_presigned_url("test_file.txt") assert url is not None assert url.startswith( @@ -73,7 +73,7 @@ def test_create_presigned_url(): ) -def test_is_url_valid(): +def test_is_url_valid(tmp_path): with mock_aws(), patch.object(AWSHandler, "_s3_client") as mock_client: presigned_url = "https://s3.us-west-2.amazonaws.com/test_bucket/test_folder/test_file.txt?query=string" mock_client.generate_presigned_url.return_value = presigned_url @@ -87,9 +87,9 @@ def test_is_url_valid(): Bucket="test_bucket", CreateBucketConfiguration={"LocationConstraint": "us-west-2"}, ) - with open("test_file.txt", "w") as file: - file.write("test file") - aws_handler.upload_file("test_file.txt") + test_file = tmp_path / "test_file.txt" + test_file.write_text("test file") + aws_handler.upload_file(str(test_file)) url = aws_handler.create_presigned_url("test_file.txt") assert aws_handler.is_url_valid(url) is True assert aws_handler.is_url_valid("invalid_url") is False diff --git a/cellpack/tests/test_data_doc.py b/cellpack/tests/test_data_doc.py index 072f5c894..6f1e563fb 100644 --- a/cellpack/tests/test_data_doc.py +++ b/cellpack/tests/test_data_doc.py @@ -45,3 +45,69 @@ def test_generate_hash(): generated_hash = DataDoc.generate_hash(input_data) assert isinstance(generated_hash, str) assert generated_hash == DataDoc.generate_hash(input_data) + + +def test_generate_hash_is_stable_across_key_order(): + recipe_a = {"name": "test", "version": "1.0", "count": 1} + recipe_b = {"count": 1, "version": "1.0", "name": "test"} + assert DataDoc.generate_hash(recipe_a) == DataDoc.generate_hash(recipe_b) + + +def test_generate_hash_is_stable_across_string_list_order(): + recipe_a = { + "composition": { + "space": {"regions": {"interior": ["A", "B", "C", "D", "E"]}}, + "A": {"object": "sphere_100", "count": 6}, + "B": {"object": "sphere_200", "count": 2}, + "C": {"object": "sphere_50", "count": 15}, + } + } + recipe_b = { + "composition": { + "A": {"count": 6, "object": "sphere_100"}, + "C": {"object": "sphere_50", "count": 15}, + "B": {"object": "sphere_200", "count": 2}, + "space": {"regions": {"interior": ["E", "C", "A", "D", "B"]}}, + } + } + assert DataDoc.generate_hash(recipe_a) == DataDoc.generate_hash(recipe_b) + + +def test_generate_hash_preserves_positional_list_order(): + # numeric/nested lists encode positional data (bounding boxes, vectors, colors) and must remain order-sensitive. + bbox_a = {"bounding_box": [[0, 0, 0], [1000, 1000, 1]]} + bbox_b = {"bounding_box": [[1000, 1000, 1], [0, 0, 0]]} + assert DataDoc.generate_hash(bbox_a) != DataDoc.generate_hash(bbox_b) + + axis_a = {"rotation_axis": [0, 0, 1]} + axis_b = {"rotation_axis": [1, 0, 0]} + assert DataDoc.generate_hash(axis_a) != DataDoc.generate_hash(axis_b) + + +def test_generate_hash_is_stable_across_mixed_list_order(): + # region lists that mix string refs with inline dicts should dedup regardless of element order. + recipe_a = { + "composition": { + "bounding_area": { + "regions": { + "interior": [ + "outer_sphere", + {"object": "green_sphere", "count": 5}, + ] + } + } + } + } + recipe_b = { + "composition": { + "bounding_area": { + "regions": { + "interior": [ + {"object": "green_sphere", "count": 5}, + "outer_sphere", + ] + } + } + } + } + assert DataDoc.generate_hash(recipe_a) == DataDoc.generate_hash(recipe_b) diff --git a/cellpack/tests/test_db_recipe_loader.py b/cellpack/tests/test_db_recipe_loader.py index 7d87cdd4f..ccf25f208 100644 --- a/cellpack/tests/test_db_recipe_loader.py +++ b/cellpack/tests/test_db_recipe_loader.py @@ -91,11 +91,13 @@ "version": "linear", "bounding_box": [[-110, -45, -62], [110, 45, 62]], "name": "test_recipe", + "description": "test_description", } compiled_firebase_recipe_example = { "name": "test_recipe", + "description": "test_description", "format_version": "2.1", "version": "linear", "bounding_box": [[-110, -45, -62], [110, 45, 62]], diff --git a/cellpack/tests/test_db_uploader.py b/cellpack/tests/test_db_uploader.py index 9ffb589fa..5d3ee4d78 100644 --- a/cellpack/tests/test_db_uploader.py +++ b/cellpack/tests/test_db_uploader.py @@ -1,3 +1,4 @@ +from cellpack.autopack.AWSHandler import AWSHandler from cellpack.autopack.DBRecipeHandler import DBUploader from cellpack.tests.mocks.mock_db import MockDB from unittest.mock import MagicMock, patch @@ -27,6 +28,7 @@ def test_upload_data_with_recipe_and_id(): collection = "recipe" data = { "name": "test", + "description": "test_description", "bounding_box": [[0, 0, 0], [1000, 1000, 1]], "version": "1.0.0", "composition": {"test": {"inherit": "firebase:test_collection/test_id"}}, @@ -147,11 +149,13 @@ def test_upload_collections(): def test_upload_recipe(): recipe_meta_data = { "name": "one_sphere", + "description": "test_description", "version": "1.0.0", "composition": {}, } recipe_data = { "name": "one_sphere", + "description": "test_description", "version": "1.0.0", "objects": { "sphere_25": { @@ -172,3 +176,55 @@ def test_upload_recipe(): "A": "firebase:composition/test_id", } assert recipe_doc.objects_to_path_map == {"sphere_25": "firebase:objects/test_id"} + + +def test_upload_job_status_with_firebase_handler(): + mock_firebase_db = MagicMock() + mock_firebase_db.create_timestamp.return_value = "test_timestamp" + + uploader = DBUploader(mock_firebase_db) + uploader.upload_job_status("test_hash", "RUNNING") + + mock_firebase_db.create_timestamp.assert_called_once() + mock_firebase_db.update_or_create.assert_called_once_with( + "job_status", + "test_hash", + { + "timestamp": "test_timestamp", + "status": "RUNNING", + "error_message": None, + }, + ) + + +def test_upload_job_status_with_aws_handler(): + mock_aws_db = MagicMock(spec=AWSHandler, wraps=None) + # Allow create_timestamp to be checked even though it's not on AWSHandler + mock_aws_db.create_timestamp = MagicMock() + + mock_firebase_handler = MagicMock() + mock_firebase_handler.create_timestamp.return_value = "firebase_timestamp" + + with patch( + "cellpack.autopack.DBRecipeHandler.DATABASE_IDS.handlers" + ) as mock_handlers: + mock_handlers.return_value.get.return_value = ( + lambda default_db: mock_firebase_handler + ) + + uploader = DBUploader(mock_aws_db) + uploader.upload_job_status("test_hash", "DONE", result_path="test_path") + + mock_firebase_handler.create_timestamp.assert_called_once() + mock_firebase_handler.update_or_create.assert_called_once_with( + "job_status", + "test_hash", + { + "timestamp": "firebase_timestamp", + "status": "DONE", + "error_message": None, + "result_path": "test_path", + }, + ) + # AWS handler should not be called for timestamp + mock_aws_db.create_timestamp.assert_not_called() diff --git a/cellpack/tests/test_gradient_data.py b/cellpack/tests/test_gradient_data.py index 3cb5a70ed..cc2457f24 100644 --- a/cellpack/tests/test_gradient_data.py +++ b/cellpack/tests/test_gradient_data.py @@ -4,6 +4,7 @@ Docs: https://docs.pytest.org/en/latest/example/simple.html https://docs.pytest.org/en/latest/plugins.html#requiring-loading-plugins-in-a-test-module-or-conftest-file """ + import pytest from cellpack.autopack.interface_objects import GradientData diff --git a/cellpack/tests/test_pack_cli.py b/cellpack/tests/test_pack_cli.py new file mode 100644 index 000000000..add6c0a5d --- /dev/null +++ b/cellpack/tests/test_pack_cli.py @@ -0,0 +1,90 @@ +""" +Integration tests for the `pack` CLI entry point (`cellpack/bin/pack.py`). + +Two input types are covered: + + 1. A string file path — the existing local CLI workflow invoked as + `pack -r RECIPE_PATH -c CONFIG_PATH`. Accepting a recipe dict must not change anything about this + path. + + 2. A json dict — the new flow used by the docker server's + `pack_handler` when it receives a json body. The dict must flow + through `RecipeLoader` and the rest of the pipeline remains the same to a + recipe loaded. + +The packing config can be supplied as a file path or omitted entirely, in +which case `ConfigLoader` falls back to its built-in default values. +""" + +import json +from pathlib import Path +import copy +import pytest + +from cellpack.bin.pack import pack + +_RECIPE = { + "version": "1.0.0", + "format_version": "2.0", + "name": "test_pack_cli", + "bounding_box": [[0, 0, 0], [50, 50, 1]], + "objects": { + "sphere_5": { + "type": "single_sphere", + "radius": 5, + "max_jitter": [1, 1, 0], + "place_method": "jitter", + } + }, + "composition": { + "space": {"regions": {"interior": ["A"]}}, + "A": {"object": "sphere_5", "count": 1}, + }, +} + + +@pytest.fixture +def recipe_data(): + # RecipeLoader mutates the dict it receives, so each test gets a fresh copy to stay independent of run order. + return copy.deepcopy(_RECIPE) + + +def _write_config(tmp_path: Path) -> Path: + config = { + "name": "test_pack_cli", + "out": f"{tmp_path}/", + "place_method": "jitter", + "inner_grid_method": "raytrace", + "save_analyze_result": False, + "save_plot_figures": False, + "number_of_packings": 1, + "show_progress_bar": False, + "load_from_grid_file": False, + } + config_path = tmp_path / "config.json" + config_path.write_text(json.dumps(config)) + return config_path + + +def test_pack_with_recipe_path(tmp_path, recipe_data): + recipe_path = tmp_path / "recipe.json" + recipe_path.write_text(json.dumps(recipe_data)) + config_path = _write_config(tmp_path) + pack(recipe=str(recipe_path), config_path=str(config_path)) + + +def test_pack_with_recipe_dict(tmp_path, recipe_data): + """ + `pack()` also accepts a recipe dict directly, so + the docker server can forward a parsed JSON body without writing it to + db first. + """ + config_path = _write_config(tmp_path) + pack(recipe=recipe_data, config_path=str(config_path)) + + +def test_pack_with_default_config(tmp_path, monkeypatch, recipe_data): + """Omitting `config_path` falls back to `ConfigLoader.default_values`.""" + # default `out: "out/"` is relative, monkeypatch.chdir keeps outputs inside tmp_path. + monkeypatch.chdir(tmp_path) + pack(recipe=recipe_data) diff --git a/cellpack/tests/test_partners.py b/cellpack/tests/test_partners.py index a4838b820..1ce91998b 100644 --- a/cellpack/tests/test_partners.py +++ b/cellpack/tests/test_partners.py @@ -6,6 +6,7 @@ Docs: https://docs.pytest.org/en/latest/ https://docs.pytest.org/en/latest/goodpractices.html#conventions-for-python-test-discovery """ + import pytest from cellpack.autopack.ingredient.agent import Agent from cellpack.autopack.interface_objects import Partners diff --git a/cellpack/tests/test_recipe_loader.py b/cellpack/tests/test_recipe_loader.py index 925f0a966..68d916dbe 100644 --- a/cellpack/tests/test_recipe_loader.py +++ b/cellpack/tests/test_recipe_loader.py @@ -4,7 +4,9 @@ Docs: https://docs.pytest.org/en/latest/example/simple.html https://docs.pytest.org/en/latest/plugins.html#requiring-loading-plugins-in-a-test-module-or-conftest-file """ + import pytest +from cellpack.autopack.interface_objects import DEFAULT_GRADIENT_MODE_SETTINGS from cellpack.autopack.loaders.recipe_loader import RecipeLoader test_objects = { @@ -93,3 +95,34 @@ def test_resolve_objects(): ) def test_sanitize_format_version(expected_result, input_recipe_data): assert expected_result == RecipeLoader._sanitize_format_version(input_recipe_data) + + +def test_normalize_gradients_fills_defaults_for_under_specified_v2_1_gradient(): + # a v2.1 recipe authored directly skips migration, so an under-specified + # gradient reaches normalization missing the default keys + gradients = {"my_gradient": {"mode": "surface"}} + + normalized = RecipeLoader._normalize_gradients(gradients) + + assert isinstance(normalized, list) + gradient = normalized[0] + assert gradient["name"] == "my_gradient" + assert gradient["mode"] == "surface" + for key in ("weight_mode", "pick_mode", "mode_settings", "weight_mode_settings"): + assert key in gradient + assert gradient["weight_mode"] == DEFAULT_GRADIENT_MODE_SETTINGS["weight_mode"] + + +def test_normalize_gradients_preserves_authored_values_and_normalizes_list_input(): + # firebase recipes already store gradients as a list of dicts + gradients = [{"name": "test", "mode": "surface", "weight_mode": "exponential"}] + + normalized = RecipeLoader._normalize_gradients(gradients) + + assert normalized[0]["weight_mode"] == "exponential" # not overwritten by default + assert normalized[0]["pick_mode"] == DEFAULT_GRADIENT_MODE_SETTINGS["pick_mode"] + + +def test_normalize_gradients_passes_through_empty(): + assert RecipeLoader._normalize_gradients(None) is None + assert RecipeLoader._normalize_gradients({}) == {} diff --git a/cellpack/tests/test_recipe_version_migration.py b/cellpack/tests/test_recipe_version_migration.py index 34f6b9751..37801c1f9 100644 --- a/cellpack/tests/test_recipe_version_migration.py +++ b/cellpack/tests/test_recipe_version_migration.py @@ -5,6 +5,7 @@ Docs: https://docs.pytest.org/en/latest/example/simple.html https://docs.pytest.org/en/latest/plugins.html#requiring-loading-plugins-in-a-test-module-or-conftest-file """ + from math import pi from unittest.mock import MagicMock import pytest @@ -316,7 +317,7 @@ def test_convert_v1_to_v2( [ ( RecipeLoader( - input_file_path="cellpack/tests/recipes/v1/test_single_spheres.json" + "cellpack/tests/recipes/v1/test_single_spheres.json" ).recipe_data, { "version": "1.0", @@ -385,9 +386,7 @@ def test_migrate_version_error(): "converted_compartment_data, expected_compartment_data", [ ( - RecipeLoader( - input_file_path="cellpack/tests/recipes/v1/test_compartment.json" - ).recipe_data, + RecipeLoader("cellpack/tests/recipes/v1/test_compartment.json").recipe_data, { "version": "1.0", "format_version": "2.0", diff --git a/docker/Dockerfile.batch b/docker/Dockerfile.batch deleted file mode 100644 index 3fbec0140..000000000 --- a/docker/Dockerfile.batch +++ /dev/null @@ -1,15 +0,0 @@ -### Build image ### -FROM python:3.9 - -WORKDIR /cellpack -COPY . /cellpack - -RUN python -m pip install --upgrade pip --root-user-action=ignore -RUN python -m pip install . --root-user-action=ignore - -# Install AWS CLI -RUN apt-get update && apt-get install -y awscli - -COPY docker/entrypoint-batch.sh /usr/local/bin/ -RUN ["chmod", "+x", "/usr/local/bin/entrypoint-batch.sh"] -ENTRYPOINT ["/usr/local/bin/entrypoint-batch.sh"] \ No newline at end of file diff --git a/docker/Dockerfile.ecs b/docker/Dockerfile.ecs index 7a303c023..430c5c06b 100644 --- a/docker/Dockerfile.ecs +++ b/docker/Dockerfile.ecs @@ -4,7 +4,9 @@ WORKDIR /cellpack COPY . /cellpack RUN python -m pip install --upgrade pip --root-user-action=ignore -RUN python -m pip install . -r requirements/linux/requirements.txt --root-user-action=ignore +RUN python -m pip install uv --root-user-action=ignore +RUN uv sync --no-default-groups --group server --frozen +ENV PATH="/cellpack/.venv/bin:$PATH" EXPOSE 80 diff --git a/docker/entrypoint-batch.sh b/docker/entrypoint-batch.sh deleted file mode 100644 index a66d45a3d..000000000 --- a/docker/entrypoint-batch.sh +++ /dev/null @@ -1,20 +0,0 @@ -#!/bin/bash -e - -if [ -z "$recipe" ]; then - echo "Required recipe parameter is missing, please include recipe in Docker run script, ie: -e recipe=path/to/recipe" - exit; -else - echo "recipe passed in: '$recipe'" -fi - -cd /cellpack - -if [ -z "$config" ]; then - echo "Config parameter not included, using default value" - pack -r $recipe -d - exit; -else - echo "config passed in: '$config'" -fi - -pack -r $recipe -c $config -d diff --git a/docker/server.py b/docker/server.py index 581e0151d..9bcac0517 100644 --- a/docker/server.py +++ b/docker/server.py @@ -1,8 +1,6 @@ import asyncio from aiohttp import web -import os -import uuid -from cellpack.autopack.DBRecipeHandler import DBUploader +from cellpack.autopack.DBRecipeHandler import DataDoc, DBUploader from cellpack.autopack.interface_objects.database_ids import DATABASE_IDS from cellpack.bin.pack import pack @@ -12,41 +10,66 @@ class CellpackServer: def __init__(self): self.packing_tasks = set() - async def run_packing(self, recipe, config, job_id): - os.environ["AWS_BATCH_JOB_ID"] = job_id - self.update_job_status(job_id, "RUNNING") + def _get_firebase_handler(self, database_name="firebase"): + handler = DATABASE_IDS.handlers().get(database_name) + initialized_db = handler(default_db="staging") + if initialized_db._initialized: + return initialized_db + return None + + def job_exists(self, dedup_hash): + db = self._get_firebase_handler() + if not db: + return False + + job_status, _ = db.get_doc_by_id("job_status", dedup_hash) + return job_status is not None + + async def run_packing(self, dedup_hash, recipe, config=None): + self.update_job_status(dedup_hash, "RUNNING") try: - pack(recipe=recipe, config_path=config, docker=True) + pack(recipe=recipe, config_path=config, docker=True, hash=dedup_hash) except Exception as e: - self.update_job_status(job_id, "FAILED", error_message=str(e)) + self.update_job_status(dedup_hash, "FAILED", error_message=str(e)) - def update_job_status(self, job_id, status, result_path=None, error_message=None): - handler = DATABASE_IDS.handlers().get("firebase") - initialized_db = handler( - default_db="staging" - ) - if initialized_db._initialized: - db_uploader = DBUploader(initialized_db) - db_uploader.upload_job_status(job_id, status, result_path, error_message) + def update_job_status(self, dedup_hash, status, result_path=None, error_message=None): + db = self._get_firebase_handler() + if db: + db_uploader = DBUploader(db) + db_uploader.upload_job_status(dedup_hash, status, result_path, error_message) async def hello_world(self, request: web.Request) -> web.Response: return web.Response(text="Hello from the cellPACK server") async def health_check(self, request: web.Request) -> web.Response: - # healthcheck endpoint needed for AWS load balancer + # health check endpoint needed for AWS load balancer return web.Response() async def pack_handler(self, request: web.Request) -> web.Response: - recipe = request.rel_url.query.get("recipe") - if recipe is None: + if not (request.can_read_body and request.content_length and request.content_length > 0): raise web.HTTPBadRequest( - "Pack requests must include recipe as a query param" + "Pack requests must include a recipe in the request body" ) + + try: + recipe = await request.json() + except Exception: + raise web.HTTPBadRequest( + "Pack requests must include a valid JSON recipe in the request body" + ) + + dedup_hash = DataDoc.generate_hash(recipe) + if self.job_exists(dedup_hash): + # We've already packed this recipe, return job id immediately + # to avoid redundant packing + return web.json_response({"jobId": dedup_hash}) + config = request.rel_url.query.get("config") - job_id = str(uuid.uuid4()) # Initiate packing task to run in background - packing_task = asyncio.create_task(self.run_packing(recipe, config, job_id)) + packing_task = asyncio.create_task( + self.run_packing(dedup_hash, recipe, config) + ) # Keep track of task references to prevent them from being garbage # collected, then discard after task completion @@ -55,7 +78,7 @@ async def pack_handler(self, request: web.Request) -> web.Response: # return job id immediately, rather than wait for task to complete, # to avoid timeout issues with API gateway - return web.json_response({"jobId": job_id}) + return web.json_response({"jobId": dedup_hash}) async def init_app() -> web.Application: @@ -70,4 +93,4 @@ async def init_app() -> web.Application: ) return app -web.run_app(init_app(), host="0.0.0.0", port=SERVER_PORT) \ No newline at end of file +web.run_app(init_app(), host="0.0.0.0", port=SERVER_PORT) diff --git a/docs/CONFIG_SCHEMA.md b/docs/CONFIG_SCHEMA.md index a990eb109..caa0b198e 100644 --- a/docs/CONFIG_SCHEMA.md +++ b/docs/CONFIG_SCHEMA.md @@ -11,7 +11,7 @@ The config file controls the packing behavior. It specifies parameters such as p | `load_from_grid_file` | boolean | Load objects from a grid file | False | | | `name` | string | Name of the config | default | Used to identify this config run | | `number_of_packings` | number (>=1) | Number of independent packing replicates | 1 | | -| `open_results_in_browser` | boolean | Open results in browser after run | True | | +| `open_results_in_browser` | boolean | Open results in browser after run | False | Prerequisite: AWS s3 credentials | | `ordered_packing` | boolean | Use deterministic packing order | False | | | `out` | string | Output directory path | `"out/"` | | | `overwrite_place_method` | boolean | Override object-specific place methods | False | | @@ -26,7 +26,7 @@ The config file controls the packing behavior. It specifies parameters such as p | `show_progress_bar` | boolean | Show progress bar in terminal | False | | | `show_sphere_trees` | boolean | Visualize sphere trees | False | | | `spacing` | number | Override object spacing | None | | -| `upload_results` | boolean | Upload results to S3 | True | | +| `upload_results` | boolean | Upload results to S3 | False | Requires AWS S3 credentials to upload the result file to S3 | | | `use_periodicity` | boolean | Enable periodic boundary conditions | False | | | `version` | number | Config version number | 1.0 | For internal tracking | | `image_export_options.hollow` | boolean | Export hollow images | False | | diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index b3d32898b..7b8a9d5a2 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -15,12 +15,11 @@ Ready to contribute? Here's how to set up `cellpack` for local development. git clone git@github.com:{your_name_here}/cellpack.git ``` -3. Install the project in editable mode by following installation instructions [here](./docs/INSTALL.md). (It is also recommended to work in a virtual environment): +3. Install the project in editable mode by following installation instructions [here](./INSTALLATION.md). (It is also recommended to work in a virtual environment): ```bash cd cellpack/ - pip install -r requirements/linux/requirements.txt - pip install -e .[dev] + uv sync ``` 4. Create a branch for local development: @@ -51,7 +50,7 @@ Ready to contribute? Here's how to set up `cellpack` for local development. ### Contributing cheat sheet -1. `pip install -e .[dev]` +1. `uv sync` This will install your package in editable mode with all the required development dependencies (i.e. `tox`). diff --git a/docs/DOCKER.md b/docs/DOCKER.md index a1214a335..a590792d3 100644 --- a/docs/DOCKER.md +++ b/docs/DOCKER.md @@ -1,18 +1,13 @@ # Docker +The CellPACK server, which is used for running packings for [CellPACK Studio](https://github.com/AllenCell/cellpack-client), is run in a Docker container using a Docker image built in this repo. +## Prerequisites * Install [docker](https://docs.docker.com/v17.09/engine/installation/) * Clone the repository locally, if you haven't already: `git clone https://github.com/mesoscope/cellpack.git` * Ensure that you have valid AWS access key and secret to access the `cellpack-results` S3 bucket, usually stored in a `~/.aws/credentials` file. If you have multiple accounts in your credentials files, ensure that the desured account is the `default` option. -* We have two Dockerfiles in /docker, one that builds the Docker image to be run in AWS ECS, and one to be run in AWS Batch. To build one of the images, run: `docker build -f [DOCKERFILE-NAME] -t [CONTAINER-NAME] .` Rebuild the container if new files are added or changes are made to the codebase. -## AWS Batch Docker Image -1. Build image, running `docker build -f docker/Dockerfile.batch -t [CONTAINER-NAME] .` -2. Run packings in the container, running: `docker run -v ~/.aws:/root/.aws -e recipe=examples/recipes/v2/one_sphere.json -e config=examples/packing-configs/run.json [CONTAINER-NAME]` -3. Verify that the packing results are saved in the `cellpack-results` S3 bucket. You should see a botocore logging message indicating that the credentials were successfully loaded. - -## AWS ECS Docker Image +## Building and Running the Docker Container 1. Build image, running `docker build -f docker/Dockerfile.ecs -t [CONTAINER-NAME] .` 2. Run packings in the container, running: `docker run -v ~/.aws:/root/.aws -p 80:80 [CONTAINER-NAME]` -3. Try hitting the test endpoint on the server, by navigating to `http://0.0.0.0:8443/hello` in your browser. -4. Try running a packing on the server, by hitting the `http://0.0.0.0:80/pack?recipe=firebase:recipes/one_sphere_v_1.0.0` in your browser. -5. Verify that the packing result path was uploaded to the firebase results table, with the job id specified in the response from the request in step 4.The result simularium file can be found at the s3 path specified there. \ No newline at end of file +3. Try hitting the test endpoint on the server, by navigating to `http://0.0.0.0:80/hello` in your browser. +4. Try running a packing on the server, install and run [CellPACK Studio](https://github.com/AllenCell/cellpack-client) locally, with the [`SUBMIT_PACKING_ECS` constant](https://github.com/AllenCell/cellpack-client/blob/main/src/constants/aws.ts) pointing to your local Docker instance diff --git a/docs/INSTALLATION.md b/docs/INSTALLATION.md index cfdbe559c..3dc6cc2d1 100644 --- a/docs/INSTALLATION.md +++ b/docs/INSTALLATION.md @@ -12,8 +12,8 @@ cd /path/to/directory/ **2. Clone the repo from GitHub** ```bash -git clone git@github.com:mesoscope/cellpack-analysis.git -cd cellpack-analysis +git clone git@github.com:mesoscope/cellpack.git +cd cellpack ``` **3. Install the dependencies using uv** diff --git a/docs/RECIPE_SCHEMA.md b/docs/RECIPE_SCHEMA.md index 26f8ca28f..1245cdd1a 100644 --- a/docs/RECIPE_SCHEMA.md +++ b/docs/RECIPE_SCHEMA.md @@ -9,15 +9,18 @@ The top-level fields include metadata about the recipe, such as its name, versio | Field Path | Type | Description | Default Value | Notes | | ---------------- | ------------------------------------------------ | ---------------------------------- | ---------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- | | `name` | string | Name of the recipe | | | +| `description` | string | Description of the recipe | | | | `version` | string | Recipe version string | "default" | Version of the recipe is appended to the output file name. | | `format_version` | string | Schema format version | "1.0" | Older recipe formats do not have this field. Recipes are automatically migrated to the latest format version before packing. | | `bounding_box` | array `[[minX, minY, minZ], [maxX, maxY, maxZ]]` | Bounding box of the packing result | `[[ 0, 0, 0 ], [ 100, 100, 100 ]]` | | | `grid_file_path` | string | File path to read/write grid data | | If not specified, a grid file is created and stored at the output path. | +| `randomness_seed` | integer | Seed for random number generation | | | **Example:** ```JSON { "name": "one_sphere", + "description": "Single sphere packed within a bounding box", "version": "1.0.0", "format_version": "2.0", "bounding_box": [ diff --git a/docs/STUDIO_SITE.md b/docs/STUDIO_SITE.md new file mode 100644 index 000000000..425524f7d --- /dev/null +++ b/docs/STUDIO_SITE.md @@ -0,0 +1,14 @@ +# cellPACK Studio Site + +cellPACK studio allows users to edit example recipes, run packings, and visualize results in the browser. + +* Production site: https://cellpack.allencell.org/ +* GitHub repository: https://github.com/AllenCell/cellpack-client + +### Publishing Recipes to cellPACK Studio +To add new example recipes to the client site, the recipe and its associated metadata must be uploaded to Firebase. + +1. Set up access to the staging Firebase account, following [these instructions](https://github.com/mesoscope/cellpack/blob/main/docs/REMOTE_DATABASES.md#firebase-firestore) +2. Determine which recipe fields should be editable in the client, and create a JSON file specifying these editable fields following the schema outlined in [this example](https://github.com/mesoscope/cellpack/blob/0f140859824086d73edab008ff381b5e5717db8b/examples/client-data/example_editable_fields.json) +3. Follow cellPACK installation requirements [in README](https://github.com/mesoscope/cellpack?tab=readme-ov-file#installation) +4. Run the following script to upload necessary files to Firebase: `upload -s -r -c -f -n "Name of Recipe" -o ` diff --git a/docs/images/nm_analysis_figure_b1_res.png b/docs/images/nm_analysis_figure_b1_res.png new file mode 100644 index 000000000..1ab962b6e Binary files /dev/null and b/docs/images/nm_analysis_figure_b1_res.png differ diff --git a/docs/images/spheres_in_a_box_res.png b/docs/images/spheres_in_a_box_res.png new file mode 100644 index 000000000..170780d3a Binary files /dev/null and b/docs/images/spheres_in_a_box_res.png differ diff --git a/docs/index.md b/docs/index.md index d86e745b6..0ecc13f16 100644 --- a/docs/index.md +++ b/docs/index.md @@ -23,7 +23,8 @@ CONTRIBUTING ``` ```{include} ../README.md -:relative-docs: ./docs/ +:relative-docs: docs/ +:relative-images: ``` - {ref}`genindex` diff --git a/examples/client-data/example_editable_fields.json b/examples/client-data/example_editable_fields.json new file mode 100644 index 000000000..028473801 --- /dev/null +++ b/examples/client-data/example_editable_fields.json @@ -0,0 +1,70 @@ +{ + "editable_fields": [ + { + "name": "Display Name", + "description": "Description text", + "path": "path.to.field.in.recipe.json", + "data_type": "integer/float/string", + "input_type": "slider/dropdown/gradient" + }, + { + "name": "Endosome Count", + "description": "Number of spheres to be packed", + "path": "composition.membrane.regions.interior.1.count", + "data_type": "integer", + "input_type": "slider", + "min": 0, + "max": 300 + }, + { + "name": "Endosome Radius", + "description": "Radius of spheres", + "path": "objects.endosome.radius", + "data_type": "float", + "input_type": "slider", + "min": 0, + "max": 10, + "unit": "µm", + "conversion_factor": 0.108 + }, + { + "name": "Spatial Distribution Rule", + "description": "Choose from one of the listed gradient types", + "path": "objects.endosome.gradient", + "data_type": "gradient", + "input_type": "gradient", + "gradient_options": [ + { + "display_name": "Nuclear Bias", + "value": "nucleus_gradient", + "path": "objects.endosome.gradient", + "packing_mode": "gradient", + "packing_mode_path": "objects.endosome.packing_mode", + "strength_path": "gradients.nucleus_gradient.weight_mode_settings.decay_length", + "strength_display_name": "Decay Length", + "strength_description": "Smaller decay length indicates stronger bias", + "strength_min": 0, + "strength_max": 1 + }, + { + "display_name": "Membrane Bias", + "value": "membrane_gradient", + "path": "objects.endosome.gradient", + "packing_mode": "gradient", + "packing_mode_path": "objects.endosome.packing_mode", + "strength_path": "gradients.membrane_gradient.weight_mode_settings.decay_length", + "strength_display_name": "Decay Length", + "strength_description": "Smaller decay length indicates stronger bias", + "strength_min": 0, + "strength_max": 1 + }, + { + "display_name": "Unbiased", + "value": "random", + "path": "objects.endosome.packing_mode", + "packing_mode": "random" + } + ] + } + ] +} diff --git a/examples/packing-configs/upload_and_open_result.json b/examples/packing-configs/upload_and_open_result.json new file mode 100644 index 000000000..411d7619f --- /dev/null +++ b/examples/packing-configs/upload_and_open_result.json @@ -0,0 +1,6 @@ +{ + "name": "upload_results_and_open_in_browser", + "upload_results": true, + "open_results_in_browser": true, + "save_analyze_result": true +} diff --git a/examples/recipes/v2/BloodPlasma-no-HIV_fv2.1.json b/examples/recipes/v2/BloodPlasma-no-HIV_fv2.1.json new file mode 100644 index 000000000..df576ee0d --- /dev/null +++ b/examples/recipes/v2/BloodPlasma-no-HIV_fv2.1.json @@ -0,0 +1,954 @@ +{ + "format_version": "2.1", + "version": "1.0", + "name": "BloodPlasma-no-HIV", + "bounding_box": [ + [ + -150, + -600, + -1100 + ], + [ + 150, + 600, + 1100 + ] + ], + "objects": { + "Heparin": { + "jitter_attempts": 5, + "color": [ + 0.41568627450980394, + 0.7568627450980392, + 0.8980392156862745 + ], + "rotation_range": 6.2831, + "max_jitter": [ + 1, + 1, + 0 + ], + "perturb_axis_amplitude": 0.1, + "is_attractor": false, + "principal_vector": [ + 1, + 0, + 0 + ], + "packing_mode": "random", + "type": "multi_sphere", + "rejection_threshold": 30, + "place_method": "jitter", + "rotation_axis": null, + "use_rotation_axis": false, + "orient_bias_range": [ + 3.141592607179586, + 3.141592607179586 + ], + "representations": { + "atomic": { + "id": "3irl", + "format": ".pdb" + }, + "packing": { + "path": "github:collisionTrees", + "name": "2hhb_hemoglobin.sph", + "format": ".sph" + }, + "mesh": { + "path": "github:geometries", + "name": "Heparin_1.dae", + "format": ".dae", + "coordinate_system": "left" + } + } + }, + "IgG_Antibody_1mer": { + "jitter_attempts": 5, + "rotation_range": 6.2831, + "color": null, + "max_jitter": [ + 1, + 1, + 0 + ], + "principal_vector": [ + 1, + 0, + 0 + ], + "perturb_axis_amplitude": 0.1, + "is_attractor": false, + "packing_mode": "random", + "type": "multi_sphere", + "rejection_threshold": 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false, + "orient_bias_range": [ + 3.141592607179586, + 3.141592607179586 + ], + "representations": { + "atomic": { + "id": "3gau", + "format": ".pdb" + }, + "packing": { + "path": "github:collisionTrees", + "name": "3gau_FactorH3.sph", + "format": ".sph" + }, + "mesh": { + "path": "github:geometries", + "name": "FactorH1_1.dae", + "format": ".dae", + "coordinate_system": "left" + } + } + }, + "i7aat_91kD": { + "jitter_attempts": 5, + "rotation_range": 6.2831, + "color": null, + "max_jitter": [ + 1, + 1, + 0 + ], + "principal_vector": [ + 1, + 0, + 0 + ], + "perturb_axis_amplitude": 0.1, + "is_attractor": false, + "packing_mode": "random", + "type": "multi_sphere", + "rejection_threshold": 30, + "place_method": "jitter", + "rotation_axis": null, + "use_rotation_axis": false, + "orient_bias_range": [ + 3.141592607179586, + 3.141592607179586 + ], + "representations": { + "atomic": { + "id": "7aat", + "format": ".pdb" + }, + "packing": { + "path": "github:collisionTrees", + "name": "7aat_91kD.sph", + "format": ".sph" + }, + "mesh": { + "path": "github:geometries", + "name": "i7aat_91kD_1.dae", + "format": ".dae", + "coordinate_system": "left" + } + } + }, + "iIgM_Antibody_5mer": { + "jitter_attempts": 5, + "rotation_range": 6.2831, + "color": null, + "max_jitter": [ + 1, + 1, + 0 + ], + "principal_vector": [ + 1, + 0, + 0 + ], + "perturb_axis_amplitude": 0.1, + "is_attractor": false, + "packing_mode": "random", + "type": "multi_sphere", + "rejection_threshold": 30, + "place_method": "jitter", + "rotation_axis": null, + "use_rotation_axis": false, + "orient_bias_range": [ + 3.141592607179586, + 3.141592607179586 + ], + "representations": { + "atomic": { + "id": "2rcj", + "format": ".pdb" + }, + "packing": { + "path": "github:collisionTrees", + "name": "IgM_Antibody_5mer.sph", + "format": ".sph" + }, + "mesh": { + "path": "github:geometries", + "name": "iIgM_Antibody_5mer_1.dae", + "format": ".dae", + "coordinate_system": "left" + } + } + }, + "Transferrin": { + "jitter_attempts": 5, + "rotation_range": 6.2831, + "color": [ + 0.17254901960784313, + 0.7568627450980392, + 0.00784313725490196 + ], + "max_jitter": [ + 1, + 1, + 0 + ], + "principal_vector": [ + 1, + 0, + 0 + ], + "perturb_axis_amplitude": 0.1, + "is_attractor": false, + "packing_mode": "random", + "type": "multi_sphere", + "rejection_threshold": 30, + "place_method": "jitter", + "rotation_axis": null, + "use_rotation_axis": false, + "orient_bias_range": [ + 3.141592607179586, + 3.141592607179586 + ], + "representations": { + "atomic": { + "id": "1lfg", + "format": ".pdb" + }, + "packing": { + "path": "github:collisionTrees", + "name": "1lfg.sph", + "format": ".sph" + }, + "mesh": { + "path": "github:geometries", + "name": "Transferrin_1.dae", + "format": ".dae", + "coordinate_system": "left" + } + } + }, + "i1smd_56kD": { + "jitter_attempts": 5, + "rotation_range": 6.2831, + "color": [ + 0.7529411764705882, + 0.7647058823529411, + 0.7450980392156863 + ], + "max_jitter": [ + 1, + 1, + 0 + ], + "principal_vector": [ + 1, + 0, + 0 + ], + "perturb_axis_amplitude": 0.1, + "is_attractor": false, + "packing_mode": "random", + "type": "multi_sphere", + "rejection_threshold": 30, + "place_method": "jitter", + "rotation_axis": null, + "use_rotation_axis": false, + "orient_bias_range": [ + 3.141592607179586, + 3.141592607179586 + ], + "representations": { + "atomic": { + "id": "1smd", + "format": ".pdb" + }, + "packing": { + "path": "github:collisionTrees", + "name": "1smd_56kD.sph", + "format": ".sph" + }, + "mesh": { + "path": "github:geometries", + "name": "i1smd_56kD_1.dae", + "format": ".dae", + "coordinate_system": "left" + } + } + } + }, + "composition": { + "space": { + "regions": { + "interior": [ + { + "object": "Heparin", + "count": 2, + "priority": -2 + }, + { + "object": "IgG_Antibody_1mer", + "count": 109, + "priority": 2 + }, + { + "object": "dLDL", + "count": 2, + "priority": -3 + }, + { + "object": "AntiTrypsin", + "count": 70, + "priority": 0.093310084 + }, + { + "object": "Ceruloplasmin", + "count": 3, + "priority": 0.12052907 + }, + { + "object": "Hemoglobin", + "count": 1, + "priority": 0.10002977 + }, + { + "object": "i2tsc_63kD", + "count": 40, + "priority": 0.097860758 + }, + { + "object": "Fibrinogen", + "count": 15, + "priority": -2 + }, + { + "object": "i1ysx_23kD", + "count": 10, + "priority": 0.082762727 + }, + { + "object": "SerumAlbumin", + "count": 805, + "priority": 0.11814741 + }, + { + "object": "iLDL", + "count": 2, + "priority": -3 + }, + { + "object": "iIgA_Antibody_2mer", + "count": 10, + "priority": 1 + }, + { + "object": "Insulin", + "count": 2, + "priority": 0.042997491 + }, + { + "object": "FactorH1", + "count": 4, + "priority": -2 + }, + { + "object": "i7aat_91kD", + "count": 40, + "priority": 0.12103942 + }, + { + "object": "iIgM_Antibody_5mer", + "count": 2, + "priority": -10 + }, + { + "object": "Transferrin", + "count": 40, + "priority": 0.12593034 + }, + { + "object": "i1smd_56kD", + "count": 70, + "priority": 0.097392932 + } + ] + } + } + } +} \ No newline at end of file diff --git a/examples/recipes/v2/endosome.json b/examples/recipes/v2/endosome.json index 2332dc127..065320762 100644 --- a/examples/recipes/v2/endosome.json +++ b/examples/recipes/v2/endosome.json @@ -2,6 +2,7 @@ "version": "gradient_packing", "format_version": "2.1", "name": "endosome", + "description": "Endosomes puncta (represented as spheres) packed with various biases in mesh containers, representing the cell membrane and nucleus, derived from a segmented hiPS cell.", "bounding_box": [ [ -124.39499130249024, diff --git a/examples/recipes/v2/er_peroxisome.json b/examples/recipes/v2/er_peroxisome.json index abf94a44d..348ad374f 100644 --- a/examples/recipes/v2/er_peroxisome.json +++ b/examples/recipes/v2/er_peroxisome.json @@ -2,6 +2,7 @@ "version": "gradient_packing", "format_version": "2.1", "name": "ER_peroxisome", + "description": "Peroxisome puncta (represented as spheres) packed in and around mesh containers representing the cell membrane, the nucleus, and the endoplasmic reticulum (ER), derived from a segmented hiPS cell.", "bounding_box": [ [ 33.77499999999999, diff --git a/examples/recipes/v2/golgi_endosome.json b/examples/recipes/v2/golgi_endosome.json index 2f84d4373..d4fcd99ad 100644 --- a/examples/recipes/v2/golgi_endosome.json +++ b/examples/recipes/v2/golgi_endosome.json @@ -2,6 +2,7 @@ "version": "gradient_packing", "format_version": "2.1", "name": "golgi_endosome", + "description": "Endosome puncta (represented as spheres) packed in and around mesh containers representing the cell membrane, the nucleus, and the Golgi, derived from a segmented hiPS cell.", "bounding_box": [ [ 34.5, diff --git a/examples/recipes/v2/one_sphere.json b/examples/recipes/v2/one_sphere.json index fe34063fd..959f7af57 100644 --- a/examples/recipes/v2/one_sphere.json +++ b/examples/recipes/v2/one_sphere.json @@ -4,14 +4,14 @@ "name": "one_sphere", "bounding_box": [ [ - 0, - 0, - 0 + -20, + -20, + -20 ], [ - 20, - 20, - 20 + 100, + 100, + 100 ] ], "objects": { @@ -58,7 +58,7 @@ 0.5, 0.5 ], - "radius": 5, + "radius": 40, "max_jitter": [ 1, 1, diff --git a/examples/recipes/v2/peroxisome.json b/examples/recipes/v2/peroxisome.json index 3d3be8641..e89c297e4 100644 --- a/examples/recipes/v2/peroxisome.json +++ b/examples/recipes/v2/peroxisome.json @@ -2,6 +2,7 @@ "version": "gradient_packing", "format_version": "2.1", "name": "peroxisome", + "description": "Peroxisomes puncta (represented as spheres) packed with various biases in mesh containers representing the cell membrane and nucleus derived from a segmented hiPS cell.", "bounding_box": [ [ 35.325, diff --git a/examples/recipes/v2/spheres_in_a_box.json b/examples/recipes/v2/spheres_in_a_box.json index 4f09db7e7..0de13949a 100644 --- a/examples/recipes/v2/spheres_in_a_box.json +++ b/examples/recipes/v2/spheres_in_a_box.json @@ -2,6 +2,7 @@ "version": "1.0.0", "format_version": "2.0", "name": "spheres_in_a_box", + "description": "Multiple spheres packed within a bounding box.", "bounding_box": [ [ 0, diff --git a/pyproject.toml b/pyproject.toml index 0fdfa0244..6a0813c2c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,6 +30,7 @@ dependencies = [ "pandas", "plotly", "pycollada", + "pydantic", "pymunk", "python-dotenv", "rtree", @@ -79,6 +80,9 @@ docs = [ "linkify-it-py", "myst-parser", ] +server = [ + "aiohttp", +] [build-system] requires = ["uv_build>=0.8.14,<0.9.0"] @@ -96,7 +100,6 @@ source-include = [ "docker", "docs", "examples", - "requirements", ".dockerignore", "tests", "__init__.py", @@ -125,6 +128,7 @@ source-exclude = [ ] [tool.black] +target-version = ["py311"] line-length = 88 [tool.isort] diff --git a/requirements/linux/requirements.txt b/requirements/linux/requirements.txt deleted file mode 100644 index 9e648b015..000000000 --- a/requirements/linux/requirements.txt +++ /dev/null @@ -1,573 +0,0 @@ -# This file was autogenerated by uv via the following command: -# uv export --no-hashes --format requirements-txt --output-file requirements/linux/requirements.txt --e . -alabaster==1.0.0 - # via sphinx -annotated-types==0.7.0 - # via pydantic -anyio==4.10.0 - # via httpx -appnope==0.1.4 ; sys_platform == 'darwin' - # via ipykernel -asttokens==3.0.0 - # via stack-data -babel==2.17.0 - # via sphinx -bioio==3.0.0 - # via cellpack -bioio-base==3.0.0 - # via - # bioio - # bioio-ome-tiff -bioio-ome-tiff==1.4.0 - # via cellpack -black==25.1.0 -boto3==1.40.19 - # via - # cellpack - # moto -botocore==1.40.19 - # via - # boto3 - # moto - # s3transfer -bumpver==2025.1131 -cachecontrol==0.14.3 - # via firebase-admin -cachetools==5.5.2 - # via - # google-auth - # tox -certifi==2025.8.3 - # via - # httpcore - # httpx - # requests -cffi==1.17.1 - # via - # cryptography - # pymunk - # pyzmq -chardet==5.2.0 - # via tox -charset-normalizer==3.4.3 - # via requests -click==8.2.1 - # via - # black - # bumpver - # dask - # distributed -cloudpickle==3.1.1 - # via - # dask - # distributed -colorama==0.4.6 - # via - # bumpver - # click - # ipython - # pytest - # sphinx - # tox - # tqdm -comm==0.2.3 - # via ipykernel -contourpy==1.3.3 - # via matplotlib -coverage==7.10.5 - # via pytest-cov -crc32c==2.7.1 - # via numcodecs -cryptography==45.0.6 - # via - # moto - # pyjwt -cycler==0.12.1 - # via matplotlib -dask==2025.9.1 - # via - # bioio - # bioio-base - # bioio-ome-tiff - # distributed -debugpy==1.8.16 - # via ipykernel -decorator==5.2.1 - # via ipython -distlib==0.4.0 - # via virtualenv -distributed==2025.9.1 - # via dask -docutils==0.21.2 - # via - # myst-parser - # sphinx - # sphinx-rtd-theme -donfig==0.8.1.post1 - # via zarr -elementpath==5.0.4 - # via xmlschema -executing==2.2.0 - # via stack-data -filelock==3.19.1 - # via - # tox - # virtualenv -fire==0.7.1 - # via cellpack -firebase-admin==7.1.0 - # via cellpack -flake8==7.3.0 - # via flake8-debugger -flake8-debugger==4.1.2 -flexcache==0.3 - # via pint -flexparser==0.4 - # via pint -fonttools==4.59.2 - # via matplotlib -fsspec==2025.9.0 - # via - # bioio-base - # bioio-ome-tiff - # dask - # kerchunk - # tifffile -google-api-core==2.25.1 - # via - # firebase-admin - # google-cloud-core - # google-cloud-firestore - # google-cloud-storage -google-auth==2.40.3 - # via - # google-api-core - # google-cloud-core - # google-cloud-firestore - # google-cloud-storage -google-cloud-core==2.4.3 - # via - # google-cloud-firestore - # google-cloud-storage -google-cloud-firestore==2.21.0 ; platform_python_implementation != 'PyPy' - # via firebase-admin -google-cloud-storage==3.3.0 - # via firebase-admin -google-crc32c==1.7.1 - # via - # google-cloud-storage - # google-resumable-media -google-resumable-media==2.7.2 - # via google-cloud-storage -googleapis-common-protos==1.70.0 - # via - # google-api-core - # grpcio-status -grpcio==1.74.0 - # via - # cellpack - # google-api-core - # grpcio-status -grpcio-status==1.74.0 - # via google-api-core -h11==0.16.0 - # via httpcore -h2==4.3.0 - # via httpx -hpack==4.1.0 - # via h2 -httpcore==1.0.9 - # via httpx -httpx==0.28.1 - # via firebase-admin -hyperframe==6.1.0 - # via h2 -idna==3.10 - # via - # anyio - # httpx - # requests -imagecodecs==2025.8.2 - # via bioio-ome-tiff -imagesize==1.4.1 - # via sphinx -importlib-metadata==8.7.0 - # via dask -iniconfig==2.1.0 - # via pytest -ipykernel==6.30.1 -ipython==9.4.0 - # via ipykernel -ipython-pygments-lexers==1.1.1 - # via ipython -jedi==0.19.2 - # via ipython -jinja2==3.1.6 - # via - # distributed - # moto - # myst-parser - # sphinx -jmespath==1.0.1 - # via - # boto3 - # botocore -jupyter-client==8.6.3 - # via ipykernel -jupyter-core==5.8.1 - # via - # ipykernel - # jupyter-client -kerchunk==0.2.9 - # via tifffile -kiwisolver==1.4.9 - # via matplotlib -lexid==2021.1006 - # via bumpver -linkify-it-py==2.0.3 -locket==1.0.0 - # via - # distributed - # partd -lxml==6.0.2 - # via ome-types -markdown-it-py==3.0.0 - # via - # mdit-py-plugins - # myst-parser -markupsafe==3.0.2 - # via - # jinja2 - # werkzeug -matplotlib==3.10.5 - # via cellpack -matplotlib-inline==0.1.7 - # via - # ipykernel - # ipython -mccabe==0.7.0 - # via flake8 -mdit-py-plugins==0.5.0 - # via myst-parser -mdurl==0.1.2 - # via markdown-it-py -mdutils==1.8.0 - # via cellpack -moto==5.1.11 -msgpack==1.1.1 - # via - # cachecontrol - # distributed -mypy-extensions==1.1.0 - # via black -myst-parser==4.0.1 -narwhals==2.2.0 - # via plotly -nest-asyncio==1.6.0 - # via ipykernel -numcodecs==0.16.3 - # via - # kerchunk - # zarr -numpy==2.3.2 - # via - # bioio - # bioio-base - # bioio-ome-tiff - # cellpack - # contourpy - # dask - # imagecodecs - # kerchunk - # matplotlib - # numcodecs - # pandas - # pycollada - # scipy - # simulariumio - # tifffile - # trimesh - # xarray - # zarr -ome-types==0.6.1 - # via - # bioio - # bioio-base - # bioio-ome-tiff -packaging==25.0 - # via - # black - # dask - # distributed - # ipykernel - # matplotlib - # plotly - # pyproject-api - # pytest - # sphinx - # tox - # xarray - # zarr -pandas==2.3.2 - # via - # cellpack - # simulariumio - # xarray -parso==0.8.5 - # via jedi -partd==1.4.2 - # via dask -pathspec==0.12.1 - # via black -pexpect==4.9.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' - # via ipython -pillow==11.3.0 - # via matplotlib -pint==0.25 - # via simulariumio -platformdirs==4.4.0 - # via - # black - # jupyter-core - # pint - # tox - # virtualenv -plotly==6.3.0 - # via cellpack -pluggy==1.6.0 - # via - # pytest - # pytest-cov - # tox -prompt-toolkit==3.0.52 - # via ipython -proto-plus==1.26.1 - # via - # google-api-core - # google-cloud-firestore -protobuf==6.32.0 - # via - # google-api-core - # google-cloud-firestore - # googleapis-common-protos - # grpcio-status - # proto-plus -psutil==7.0.0 - # via - # distributed - # ipykernel -ptyprocess==0.7.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' - # via pexpect -pure-eval==0.2.3 - # via stack-data -pyasn1==0.6.1 - # via - # pyasn1-modules - # rsa -pyasn1-modules==0.4.2 - # via google-auth -pycodestyle==2.14.0 - # via - # flake8 - # flake8-debugger -pycollada==0.9.2 - # via cellpack -pycparser==2.22 - # via cffi -pydantic==2.11.9 - # via - # bioio-ome-tiff - # ome-types - # pydantic-extra-types -pydantic-core==2.33.2 - # via pydantic -pydantic-extra-types==2.10.5 - # via ome-types -pyflakes==3.4.0 - # via flake8 -pygments==2.19.2 - # via - # ipython - # ipython-pygments-lexers - # pytest - # sphinx -pyjwt==2.10.1 - # via firebase-admin -pymunk==7.1.0 - # via cellpack -pyparsing==3.2.3 - # via matplotlib -pyproject-api==1.9.1 - # via tox -pytest==8.4.1 - # via - # pytest-cov - # pytest-raises -pytest-cov==6.2.1 -pytest-raises==0.11 -python-dateutil==2.9.0.post0 - # via - # botocore - # jupyter-client - # matplotlib - # moto - # pandas - # pycollada -python-dotenv==1.1.1 - # via cellpack -pytz==2025.2 - # via pandas -pywin32==311 ; platform_python_implementation != 'PyPy' and sys_platform == 'win32' - # via jupyter-core -pyyaml==6.0.2 - # via - # bioio-ome-tiff - # dask - # distributed - # donfig - # myst-parser - # responses -pyzmq==27.0.2 - # via - # ipykernel - # jupyter-client -requests==2.32.5 - # via - # cachecontrol - # google-api-core - # google-cloud-storage - # moto - # responses - # sphinx -responses==0.25.8 - # via moto -roman-numerals-py==3.1.0 - # via sphinx -rsa==4.9.1 - # via google-auth -rtree==1.4.1 - # via cellpack -s3transfer==0.13.1 - # via boto3 -scipy==1.16.1 - # via cellpack -semver==3.0.4 - # via bioio -simulariumio==1.13.0 - # via cellpack -six==1.17.0 - # via python-dateutil -sniffio==1.3.1 - # via anyio -snowballstemmer==3.0.1 - # via sphinx -sortedcontainers==2.4.0 - # via distributed -sphinx==8.2.3 - # via - # myst-parser - # sphinx-rtd-theme - # sphinxcontrib-jquery -sphinx-rtd-theme==3.0.2 -sphinxcontrib-applehelp==2.0.0 - # via sphinx -sphinxcontrib-devhelp==2.0.0 - # via sphinx -sphinxcontrib-htmlhelp==2.1.0 - # via sphinx -sphinxcontrib-jquery==4.1 - # via sphinx-rtd-theme -sphinxcontrib-jsmath==1.0.1 - # via sphinx -sphinxcontrib-qthelp==2.0.0 - # via sphinx -sphinxcontrib-serializinghtml==2.0.0 - # via sphinx -stack-data==0.6.3 - # via ipython -tblib==3.1.0 - # via distributed -termcolor==3.1.0 - # via fire -tifffile==2025.9.20 - # via bioio-ome-tiff -toml==0.10.2 - # via bumpver -tomli==2.2.1 ; python_full_version <= '3.11' - # via coverage -toolz==1.0.0 - # via - # dask - # distributed - # partd -tornado==6.5.2 - # via - # distributed - # ipykernel - # jupyter-client -tox==4.27.0 -tqdm==4.67.1 - # via cellpack -traitlets==5.14.3 - # via - # ipykernel - # ipython - # jupyter-client - # jupyter-core - # matplotlib-inline -trimesh==4.7.4 - # via cellpack -typing-extensions==4.15.0 - # via - # anyio - # flexcache - # flexparser - # ipython - # numcodecs - # pint - # pydantic - # pydantic-core - # pydantic-extra-types - # typing-inspection - # xsdata - # zarr -typing-inspection==0.4.1 - # via pydantic -tzdata==2025.2 - # via pandas -uc-micro-py==1.0.3 - # via linkify-it-py -ujson==5.11.0 - # via kerchunk -urllib3==2.5.0 - # via - # botocore - # distributed - # requests - # responses -virtualenv==20.34.0 - # via tox -wcwidth==0.2.13 - # via prompt-toolkit -werkzeug==3.1.3 - # via moto -wheel==0.45.1 -xarray==2025.9.0 - # via - # bioio-base - # bioio-ome-tiff -xmlschema==4.1.0 - # via bioio-ome-tiff -xmltodict==0.14.2 - # via moto -xsdata==24.3.1 - # via ome-types -zarr==3.1.3 - # via - # kerchunk - # tifffile -zict==3.0.0 - # via distributed -zipp==3.23.0 - # via importlib-metadata diff --git a/requirements/macos/requirements.txt b/requirements/macos/requirements.txt deleted file mode 100644 index 81e319ed7..000000000 --- a/requirements/macos/requirements.txt +++ /dev/null @@ -1,573 +0,0 @@ -# This file was autogenerated by uv via the following command: -# uv export --no-hashes --format requirements-txt --output-file requirements/macos/requirements.txt --e . -alabaster==1.0.0 - # via sphinx -annotated-types==0.7.0 - # via pydantic -anyio==4.10.0 - # via httpx -appnope==0.1.4 ; sys_platform == 'darwin' - # via ipykernel -asttokens==3.0.0 - # via stack-data -babel==2.17.0 - # via sphinx -bioio==3.0.0 - # via cellpack -bioio-base==3.0.0 - # via - # bioio - # bioio-ome-tiff -bioio-ome-tiff==1.4.0 - # via cellpack -black==25.1.0 -boto3==1.40.19 - # via - # cellpack - # moto -botocore==1.40.19 - # via - # boto3 - # moto - # s3transfer -bumpver==2025.1131 -cachecontrol==0.14.3 - # via firebase-admin -cachetools==5.5.2 - # via - # google-auth - # tox -certifi==2025.8.3 - # via - # httpcore - # httpx - # requests -cffi==1.17.1 - # via - # cryptography - # pymunk - # pyzmq -chardet==5.2.0 - # via tox -charset-normalizer==3.4.3 - # via requests -click==8.2.1 - # via - # black - # bumpver - # dask - # distributed -cloudpickle==3.1.1 - # via - # dask - # distributed -colorama==0.4.6 - # via - # bumpver - # click - # ipython - # pytest - # sphinx - # tox - # tqdm -comm==0.2.3 - # via ipykernel -contourpy==1.3.3 - # via matplotlib -coverage==7.10.5 - # via pytest-cov -crc32c==2.7.1 - # via numcodecs -cryptography==45.0.6 - # via - # moto - # pyjwt -cycler==0.12.1 - # via matplotlib -dask==2025.9.1 - # via - # bioio - # bioio-base - # bioio-ome-tiff - # distributed -debugpy==1.8.16 - # via ipykernel -decorator==5.2.1 - # via ipython -distlib==0.4.0 - # via virtualenv -distributed==2025.9.1 - # via dask -docutils==0.21.2 - # via - # myst-parser - # sphinx - # sphinx-rtd-theme -donfig==0.8.1.post1 - # via zarr -elementpath==5.0.4 - # via xmlschema -executing==2.2.0 - # via stack-data -filelock==3.19.1 - # via - # tox - # virtualenv -fire==0.7.1 - # via cellpack -firebase-admin==7.1.0 - # via cellpack -flake8==7.3.0 - # via flake8-debugger -flake8-debugger==4.1.2 -flexcache==0.3 - # via pint -flexparser==0.4 - # via pint -fonttools==4.59.2 - # via matplotlib -fsspec==2025.9.0 - # via - # bioio-base - # bioio-ome-tiff - # dask - # kerchunk - # tifffile -google-api-core==2.25.1 - # via - # firebase-admin - # google-cloud-core - # google-cloud-firestore - # google-cloud-storage -google-auth==2.40.3 - # via - # google-api-core - # google-cloud-core - # google-cloud-firestore - # google-cloud-storage -google-cloud-core==2.4.3 - # via - # google-cloud-firestore - # google-cloud-storage -google-cloud-firestore==2.21.0 ; platform_python_implementation != 'PyPy' - # via firebase-admin -google-cloud-storage==3.3.0 - # via firebase-admin -google-crc32c==1.7.1 - # via - # google-cloud-storage - # google-resumable-media -google-resumable-media==2.7.2 - # via google-cloud-storage -googleapis-common-protos==1.70.0 - # via - # google-api-core - # grpcio-status -grpcio==1.74.0 - # via - # cellpack - # google-api-core - # grpcio-status -grpcio-status==1.74.0 - # via google-api-core -h11==0.16.0 - # via httpcore -h2==4.3.0 - # via httpx -hpack==4.1.0 - # via h2 -httpcore==1.0.9 - # via httpx -httpx==0.28.1 - # via firebase-admin -hyperframe==6.1.0 - # via h2 -idna==3.10 - # via - # anyio - # httpx - # requests -imagecodecs==2025.8.2 - # via bioio-ome-tiff -imagesize==1.4.1 - # via sphinx -importlib-metadata==8.7.0 - # via dask -iniconfig==2.1.0 - # via pytest -ipykernel==6.30.1 -ipython==9.4.0 - # via ipykernel -ipython-pygments-lexers==1.1.1 - # via ipython -jedi==0.19.2 - # via ipython -jinja2==3.1.6 - # via - # distributed - # moto - # myst-parser - # sphinx -jmespath==1.0.1 - # via - # boto3 - # botocore -jupyter-client==8.6.3 - # via ipykernel -jupyter-core==5.8.1 - # via - # ipykernel - # jupyter-client -kerchunk==0.2.9 - # via tifffile -kiwisolver==1.4.9 - # via matplotlib -lexid==2021.1006 - # via bumpver -linkify-it-py==2.0.3 -locket==1.0.0 - # via - # distributed - # partd -lxml==6.0.2 - # via ome-types -markdown-it-py==3.0.0 - # via - # mdit-py-plugins - # myst-parser -markupsafe==3.0.2 - # via - # jinja2 - # werkzeug -matplotlib==3.10.5 - # via cellpack -matplotlib-inline==0.1.7 - # via - # ipykernel - # ipython -mccabe==0.7.0 - # via flake8 -mdit-py-plugins==0.5.0 - # via myst-parser -mdurl==0.1.2 - # via markdown-it-py -mdutils==1.8.0 - # via cellpack -moto==5.1.11 -msgpack==1.1.1 - # via - # cachecontrol - # distributed -mypy-extensions==1.1.0 - # via black -myst-parser==4.0.1 -narwhals==2.2.0 - # via plotly -nest-asyncio==1.6.0 - # via ipykernel -numcodecs==0.16.3 - # via - # kerchunk - # zarr -numpy==2.3.2 - # via - # bioio - # bioio-base - # bioio-ome-tiff - # cellpack - # contourpy - # dask - # imagecodecs - # kerchunk - # matplotlib - # numcodecs - # pandas - # pycollada - # scipy - # simulariumio - # tifffile - # trimesh - # xarray - # zarr -ome-types==0.6.1 - # via - # bioio - # bioio-base - # bioio-ome-tiff -packaging==25.0 - # via - # black - # dask - # distributed - # ipykernel - # matplotlib - # plotly - # pyproject-api - # pytest - # sphinx - # tox - # xarray - # zarr -pandas==2.3.2 - # via - # cellpack - # simulariumio - # xarray -parso==0.8.5 - # via jedi -partd==1.4.2 - # via dask -pathspec==0.12.1 - # via black -pexpect==4.9.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' - # via ipython -pillow==11.3.0 - # via matplotlib -pint==0.25 - # via simulariumio -platformdirs==4.4.0 - # via - # black - # jupyter-core - # pint - # tox - # virtualenv -plotly==6.3.0 - # via cellpack -pluggy==1.6.0 - # via - # pytest - # pytest-cov - # tox -prompt-toolkit==3.0.52 - # via ipython -proto-plus==1.26.1 - # via - # google-api-core - # google-cloud-firestore -protobuf==6.32.0 - # via - # google-api-core - # google-cloud-firestore - # googleapis-common-protos - # grpcio-status - # proto-plus -psutil==7.0.0 - # via - # distributed - # ipykernel -ptyprocess==0.7.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' - # via pexpect -pure-eval==0.2.3 - # via stack-data -pyasn1==0.6.1 - # via - # pyasn1-modules - # rsa -pyasn1-modules==0.4.2 - # via google-auth -pycodestyle==2.14.0 - # via - # flake8 - # flake8-debugger -pycollada==0.9.2 - # via cellpack -pycparser==2.22 - # via cffi -pydantic==2.11.9 - # via - # bioio-ome-tiff - # ome-types - # pydantic-extra-types -pydantic-core==2.33.2 - # via pydantic -pydantic-extra-types==2.10.5 - # via ome-types -pyflakes==3.4.0 - # via flake8 -pygments==2.19.2 - # via - # ipython - # ipython-pygments-lexers - # pytest - # sphinx -pyjwt==2.10.1 - # via firebase-admin -pymunk==7.1.0 - # via cellpack -pyparsing==3.2.3 - # via matplotlib -pyproject-api==1.9.1 - # via tox -pytest==8.4.1 - # via - # pytest-cov - # pytest-raises -pytest-cov==6.2.1 -pytest-raises==0.11 -python-dateutil==2.9.0.post0 - # via - # botocore - # jupyter-client - # matplotlib - # moto - # pandas - # pycollada -python-dotenv==1.1.1 - # via cellpack -pytz==2025.2 - # via pandas -pywin32==311 ; platform_python_implementation != 'PyPy' and sys_platform == 'win32' - # via jupyter-core -pyyaml==6.0.2 - # via - # bioio-ome-tiff - # dask - # distributed - # donfig - # myst-parser - # responses -pyzmq==27.0.2 - # via - # ipykernel - # jupyter-client -requests==2.32.5 - # via - # cachecontrol - # google-api-core - # google-cloud-storage - # moto - # responses - # sphinx -responses==0.25.8 - # via moto -roman-numerals-py==3.1.0 - # via sphinx -rsa==4.9.1 - # via google-auth -rtree==1.4.1 - # via cellpack -s3transfer==0.13.1 - # via boto3 -scipy==1.16.1 - # via cellpack -semver==3.0.4 - # via bioio -simulariumio==1.13.0 - # via cellpack -six==1.17.0 - # via python-dateutil -sniffio==1.3.1 - # via anyio -snowballstemmer==3.0.1 - # via sphinx -sortedcontainers==2.4.0 - # via distributed -sphinx==8.2.3 - # via - # myst-parser - # sphinx-rtd-theme - # sphinxcontrib-jquery -sphinx-rtd-theme==3.0.2 -sphinxcontrib-applehelp==2.0.0 - # via sphinx -sphinxcontrib-devhelp==2.0.0 - # via sphinx -sphinxcontrib-htmlhelp==2.1.0 - # via sphinx -sphinxcontrib-jquery==4.1 - # via sphinx-rtd-theme -sphinxcontrib-jsmath==1.0.1 - # via sphinx -sphinxcontrib-qthelp==2.0.0 - # via sphinx -sphinxcontrib-serializinghtml==2.0.0 - # via sphinx -stack-data==0.6.3 - # via ipython -tblib==3.1.0 - # via distributed -termcolor==3.1.0 - # via fire -tifffile==2025.9.20 - # via bioio-ome-tiff -toml==0.10.2 - # via bumpver -tomli==2.2.1 ; python_full_version <= '3.11' - # via coverage -toolz==1.0.0 - # via - # dask - # distributed - # partd -tornado==6.5.2 - # via - # distributed - # ipykernel - # jupyter-client -tox==4.27.0 -tqdm==4.67.1 - # via cellpack -traitlets==5.14.3 - # via - # ipykernel - # ipython - # jupyter-client - # jupyter-core - # matplotlib-inline -trimesh==4.7.4 - # via cellpack -typing-extensions==4.15.0 - # via - # anyio - # flexcache - # flexparser - # ipython - # numcodecs - # pint - # pydantic - # pydantic-core - # pydantic-extra-types - # typing-inspection - # xsdata - # zarr -typing-inspection==0.4.1 - # via pydantic -tzdata==2025.2 - # via pandas -uc-micro-py==1.0.3 - # via linkify-it-py -ujson==5.11.0 - # via kerchunk -urllib3==2.5.0 - # via - # botocore - # distributed - # requests - # responses -virtualenv==20.34.0 - # via tox -wcwidth==0.2.13 - # via prompt-toolkit -werkzeug==3.1.3 - # via moto -wheel==0.45.1 -xarray==2025.9.0 - # via - # bioio-base - # bioio-ome-tiff -xmlschema==4.1.0 - # via bioio-ome-tiff -xmltodict==0.14.2 - # via moto -xsdata==24.3.1 - # via ome-types -zarr==3.1.3 - # via - # kerchunk - # tifffile -zict==3.0.0 - # via distributed -zipp==3.23.0 - # via importlib-metadata diff --git a/requirements/windows/requirements.txt b/requirements/windows/requirements.txt deleted file mode 100644 index 3ceddc6f6..000000000 --- a/requirements/windows/requirements.txt +++ /dev/null @@ -1,573 +0,0 @@ -# This file was autogenerated by uv via the following command: -# uv export --no-hashes --format requirements-txt --output-file requirements/windows/requirements.txt --e . -alabaster==1.0.0 - # via sphinx -annotated-types==0.7.0 - # via pydantic -anyio==4.10.0 - # via httpx -appnope==0.1.4 ; sys_platform == 'darwin' - # via ipykernel -asttokens==3.0.0 - # via stack-data -babel==2.17.0 - # via sphinx -bioio==3.0.0 - # via cellpack -bioio-base==3.0.0 - # via - # bioio - # bioio-ome-tiff -bioio-ome-tiff==1.4.0 - # via cellpack -black==25.1.0 -boto3==1.40.19 - # via - # cellpack - # moto -botocore==1.40.19 - # via - # boto3 - # moto - # s3transfer -bumpver==2025.1131 -cachecontrol==0.14.3 - # via firebase-admin -cachetools==5.5.2 - # via - # google-auth - # tox -certifi==2025.8.3 - # via - # httpcore - # httpx - # requests -cffi==1.17.1 - # via - # cryptography - # pymunk - # pyzmq -chardet==5.2.0 - # via tox -charset-normalizer==3.4.3 - # via requests -click==8.2.1 - # via - # black - # bumpver - # dask - # distributed -cloudpickle==3.1.1 - # via - # dask - # distributed -colorama==0.4.6 - # via - # bumpver - # click - # ipython - # pytest - # sphinx - # tox - # tqdm -comm==0.2.3 - # via ipykernel -contourpy==1.3.3 - # via matplotlib -coverage==7.10.5 - # via pytest-cov -crc32c==2.7.1 - # via numcodecs -cryptography==45.0.6 - # via - # moto - # pyjwt -cycler==0.12.1 - # via matplotlib -dask==2025.9.1 - # via - # bioio - # bioio-base - # bioio-ome-tiff - # distributed -debugpy==1.8.16 - # via ipykernel -decorator==5.2.1 - # via ipython -distlib==0.4.0 - # via virtualenv -distributed==2025.9.1 - # via dask -docutils==0.21.2 - # via - # myst-parser - # sphinx - # sphinx-rtd-theme -donfig==0.8.1.post1 - # via zarr -elementpath==5.0.4 - # via xmlschema -executing==2.2.0 - # via stack-data -filelock==3.19.1 - # via - # tox - # virtualenv -fire==0.7.1 - # via cellpack -firebase-admin==7.1.0 - # via cellpack -flake8==7.3.0 - # via flake8-debugger -flake8-debugger==4.1.2 -flexcache==0.3 - # via pint -flexparser==0.4 - # via pint -fonttools==4.59.2 - # via matplotlib -fsspec==2025.9.0 - # via - # bioio-base - # bioio-ome-tiff - # dask - # kerchunk - # tifffile -google-api-core==2.25.1 - # via - # firebase-admin - # google-cloud-core - # google-cloud-firestore - # google-cloud-storage -google-auth==2.40.3 - # via - # google-api-core - # google-cloud-core - # google-cloud-firestore - # google-cloud-storage -google-cloud-core==2.4.3 - # via - # google-cloud-firestore - # google-cloud-storage -google-cloud-firestore==2.21.0 ; platform_python_implementation != 'PyPy' - # via firebase-admin -google-cloud-storage==3.3.0 - # via firebase-admin -google-crc32c==1.7.1 - # via - # google-cloud-storage - # google-resumable-media -google-resumable-media==2.7.2 - # via google-cloud-storage -googleapis-common-protos==1.70.0 - # via - # google-api-core - # grpcio-status -grpcio==1.74.0 - # via - # cellpack - # google-api-core - # grpcio-status -grpcio-status==1.74.0 - # via google-api-core -h11==0.16.0 - # via httpcore -h2==4.3.0 - # via httpx -hpack==4.1.0 - # via h2 -httpcore==1.0.9 - # via httpx -httpx==0.28.1 - # via firebase-admin -hyperframe==6.1.0 - # via h2 -idna==3.10 - # via - # anyio - # httpx - # requests -imagecodecs==2025.8.2 - # via bioio-ome-tiff -imagesize==1.4.1 - # via sphinx -importlib-metadata==8.7.0 - # via dask -iniconfig==2.1.0 - # via pytest -ipykernel==6.30.1 -ipython==9.4.0 - # via ipykernel -ipython-pygments-lexers==1.1.1 - # via ipython -jedi==0.19.2 - # via ipython -jinja2==3.1.6 - # via - # distributed - # moto - # myst-parser - # sphinx -jmespath==1.0.1 - # via - # boto3 - # botocore -jupyter-client==8.6.3 - # via ipykernel -jupyter-core==5.8.1 - # via - # ipykernel - # jupyter-client -kerchunk==0.2.9 - # via tifffile -kiwisolver==1.4.9 - # via matplotlib -lexid==2021.1006 - # via bumpver -linkify-it-py==2.0.3 -locket==1.0.0 - # via - # distributed - # partd -lxml==6.0.2 - # via ome-types -markdown-it-py==3.0.0 - # via - # mdit-py-plugins - # myst-parser -markupsafe==3.0.2 - # via - # jinja2 - # werkzeug -matplotlib==3.10.5 - # via cellpack -matplotlib-inline==0.1.7 - # via - # ipykernel - # ipython -mccabe==0.7.0 - # via flake8 -mdit-py-plugins==0.5.0 - # via myst-parser -mdurl==0.1.2 - # via markdown-it-py -mdutils==1.8.0 - # via cellpack -moto==5.1.11 -msgpack==1.1.1 - # via - # cachecontrol - # distributed -mypy-extensions==1.1.0 - # via black -myst-parser==4.0.1 -narwhals==2.2.0 - # via plotly -nest-asyncio==1.6.0 - # via ipykernel -numcodecs==0.16.3 - # via - # kerchunk - # zarr -numpy==2.3.2 - # via - # bioio - # bioio-base - # bioio-ome-tiff - # cellpack - # contourpy - # dask - # imagecodecs - # kerchunk - # matplotlib - # numcodecs - # pandas - # pycollada - # scipy - # simulariumio - # tifffile - # trimesh - # xarray - # zarr -ome-types==0.6.1 - # via - # bioio - # bioio-base - # bioio-ome-tiff -packaging==25.0 - # via - # black - # dask - # distributed - # ipykernel - # matplotlib - # plotly - # pyproject-api - # pytest - # sphinx - # tox - # xarray - # zarr -pandas==2.3.2 - # via - # cellpack - # simulariumio - # xarray -parso==0.8.5 - # via jedi -partd==1.4.2 - # via dask -pathspec==0.12.1 - # via black -pexpect==4.9.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' - # via ipython -pillow==11.3.0 - # via matplotlib -pint==0.25 - # via simulariumio -platformdirs==4.4.0 - # via - # black - # jupyter-core - # pint - # tox - # virtualenv -plotly==6.3.0 - # via cellpack -pluggy==1.6.0 - # via - # pytest - # pytest-cov - # tox -prompt-toolkit==3.0.52 - # via ipython -proto-plus==1.26.1 - # via - # google-api-core - # google-cloud-firestore -protobuf==6.32.0 - # via - # google-api-core - # google-cloud-firestore - # googleapis-common-protos - # grpcio-status - # proto-plus -psutil==7.0.0 - # via - # distributed - # ipykernel -ptyprocess==0.7.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' - # via pexpect -pure-eval==0.2.3 - # via stack-data -pyasn1==0.6.1 - # via - # pyasn1-modules - # rsa -pyasn1-modules==0.4.2 - # via google-auth -pycodestyle==2.14.0 - # via - # flake8 - # flake8-debugger -pycollada==0.9.2 - # via cellpack -pycparser==2.22 - # via cffi -pydantic==2.11.9 - # via - # bioio-ome-tiff - # ome-types - # pydantic-extra-types -pydantic-core==2.33.2 - # via pydantic -pydantic-extra-types==2.10.5 - # via ome-types 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