Consolidate scripts and python package (#238)

* some functionality from `scripts/` would be useful inside the library
* some functionality from the library was replicated in `scripts/`

-> consolidate (see also #208), turn separate scripts into entrypoints (currently prefixed with `bmp-` from Benchmark-Models-Petab)

* Reduce number of package configuration files
* replace isort/flake/... by ruff
* Problem feature table accessible through the library (closes #169)
* `--help` for the overview table entrypoint
* Extend overview table: add objective priors (Closes #232

Author: dweindl

.github/pull_request_template.md

@@ -15,8 +15,8 @@
   - [ ] The model ID and model name attributes in the SBML model file match the problem name ([example](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab/blob/3154d27edbfc4eb19b768465945bc81381a7c964/Benchmark-Models/Rahman_MBS2016/model_Rahman_MBS2016.xml#L3))
 - [ ] PEtab files
   - [ ] A "simulated data" measurement table is included, using the nominal parameters
-  - [ ] A visualization table is included, that can be used with the simulate data to reproduce figures from the original publication
+  - [ ] A visualization table is included, that can be used with the simulated data to reproduce figures from the original publication
   - [ ] The PEtab problem is valid (check with e.g. `petablint -vy problem.yaml`)
 - [ ] The PEtab problem author(s) are assigned to the GitHub issue
-- [ ] The README has been updated with `python scripts/overview.py --update`
+- [ ] The README has been updated with `bmp-create-overview  --update` (requires `pip install -e src/python/bmp` from the repository root)
   - [ ] The new PEtab problem row in the generated table has the correct reference (and other entries)

.github/workflows/tests.yml

@@ -23,16 +23,13 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install --upgrade setuptools wheel
-        pip install -r scripts/requirements.txt
+        cd src/python && pip install -e .
 
     - name: Check with petablint
-      run: ./check_petablint.py
-      working-directory: scripts/
+      run: bmp-petablint
 
     - name: Show overview
-      run: ./overview.py
-      working-directory: scripts/
+      run: bmp-create-overview
 
     - name: Check SBML metadata
-      run: ./check_sbml_metadata.py
-      working-directory: scripts/
+      run: bmp-check-sbml-metadata

.pre-commit-config.yaml

@@ -1,18 +1,40 @@
 files: src/python
 repos:
-- repo: https://github.com/psf/black
-  rev: 23.7.0
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.6.0
   hooks:
-  - id: black
-    description: The uncompromising code formatter
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+  - id: check-yaml
+    description: Check yaml files for parseable syntax
+  - id: check-added-large-files
+    description: Prevent large files from being committed
+  - id: check-merge-conflict
+    description: Check for files that contain merge conflict strings
+  - id: check-symlinks
+    description: Check for symlinks which do not point to anything
+  - id: check-executables-have-shebangs
+    description: Check that (non-binary) executables have shebangs
+  - id: detect-private-key
+    description: Detects the presence of private keys
+  - id: end-of-file-fixer
+    description: Fix empty lines at ends of files
+  - id: mixed-line-ending
+    description: Replace or check mixed line endings
+  - id: trailing-whitespace
+    description: Trim trailing whitespaces
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.6.7
   hooks:
-  - id: isort
-    name: isort
-- repo: https://github.com/pycqa/flake8
-  rev: 6.0.0
-  hooks:
-  - id: flake8
-    args: [--config, src/python/setup.cfg]
-    additional_dependencies: [flake8-docstrings]
+    # Run the linter.
+    - id: ruff
+      args:
+        - --fix
+        - --config
+        - src/python/pyproject.toml
+
+    # Run the formatter.
+    - id: ruff-format
+      args:
+        - --config
+        - src/python/pyproject.toml