Proposed changes to create release v0.7.0 of libCellML

.github/scripts/generate_changelog.py

@@ -14,7 +14,7 @@
     "Authorization": f"Bearer {os.environ['GH_TOKEN']}"
 }
 
-TAG_PATTERN = re.compile(r"^source-v(\d+\.\d+\.\d+)$")
+TAG_PATTERN = re.compile(r"^v(\d+\.\d+\.\d+)$")
 LABEL_PRIORITY = []
 
 
@@ -53,25 +53,29 @@ def find_previous_source_tag(end_tag):
     m = None if end_tag == "HEAD" else TAG_PATTERN.match(end_tag)
     end_version = semver.parse(m.group(1)) if m else None
 
-    print(f"Finding previous source tag before {end_tag} (version {end_version})")
+    print(f"Finding previous version tag before {end_tag} (version: {end_version})")
     for t in tags:
         m = TAG_PATTERN.match(t)
         if not m:
             continue
 
         v = semver.parse(m.group(1))
-        if end_version and v >= semver.parse(end_version):
+        if end_version and v >= end_version:
             continue
 
         valid.append((v, t))
 
     print(valid)
     if not valid:
-        raise RuntimeError("No valid source-vX.Y.Z tags found")
+        raise RuntimeError("No valid vX.Y.Z tags found")
 
     valid.sort(reverse=True)
-    print(f"Previous source tag found: {valid[0][1]} with version {valid[0][0]}")
-    return valid[0][1]
+    previous_source_tag = f"source-{valid[0][1]}"
+    if not previous_source_tag in tags:
+        raise RuntimeError(f"Previous source tag {previous_source_tag} for {valid[0][1]} not found in git tags")
+
+    print(f"Previous source tag found: {previous_source_tag} with version {valid[0][0]}")
+    return previous_source_tag
 
 
 def get_merge_commits(start, end="HEAD"):
@@ -80,19 +84,23 @@ def get_merge_commits(start, end="HEAD"):
         f"{start}..{end}",
         "--merges",
         "--first-parent",
-        "--pretty=%s"
+        "--pretty=%h"
     ])
     print(f"Git log between {start} and {end}:\n{log}")
     return log.splitlines()
 
 
-def extract_pr_numbers(messages):
-    prs = []
-    for msg in messages:
-        m = re.search(r"#(\d+)", msg)
-        if m:
-            prs.append(int(m.group(1)))
-    return prs
+def fetch_associated_pr_number(commit):
+    url = f"{GITHUB_API}/repos/cellml/libcellml/commits/{commit}/pulls"
+    r = requests.get(url, headers=HEADERS)
+    r.raise_for_status()
+    prs = r.json()
+    if not prs:
+        print(f"No associated PR found for commit {commit}.")
+        return None
+    pr_number = prs[0]["number"]
+    print(f"Associated PR #{pr_number} found for commit {commit}.")
+    return pr_number
 
 
 def fetch_pr(org_repo, pr_number):
@@ -184,9 +192,14 @@ def process_arguments():
 if __name__ == "__main__":
     args = process_arguments()
     previous_source_tag = find_previous_source_tag(args.tag_end) if args.tag_start == "PREV" else args.tag_start
-    messages = get_merge_commits(previous_source_tag, 'source-v' + args.tag_end if args.tag_end != "HEAD" else "HEAD")
-    print(f"Found {len(messages)} merge commits between {previous_source_tag} and {args.tag_end}.")
-    pr_numbers = extract_pr_numbers(messages)
+    commits = get_merge_commits(previous_source_tag, 'source-' + args.tag_end if args.tag_end != "HEAD" else "HEAD")
+    print(f"Found {len(commits)} merge commits between {previous_source_tag} and {args.tag_end}.")
+
+    pr_numbers = []
+    for commit in commits:
+        pr_number = fetch_associated_pr_number(commit)
+        if pr_number is not None:
+            pr_numbers.append(pr_number)
     print(f"Extracted {len(pr_numbers)} PR numbers from merge commits.")
 
     summaries = []
@@ -203,6 +216,6 @@ def process_arguments():
     print(f"Extracted summaries for {len(sorted_summaries)} merged PRs.")
     print(sorted_summaries)
 
-    tag_end_label = "latest" if args.tag_end == "HEAD" else f"v{args.tag_end}"
+    tag_end_label = "latest" if args.tag_end == "HEAD" else f"{args.tag_end}"
     tag_end_label = tag_end_label if args.tag_end_display_name is None else args.tag_end_display_name
     write_out_to_changelog_file(sorted_summaries, tag_end=tag_end_label)

.github/workflows/release-changelog.yml

@@ -34,7 +34,7 @@ jobs:
 
           # Extract release tag by removing prefix
           tag="${branch#${{ vars.RELEASE_STAGING_BRANCH_STEM }}}"
-          echo "RELEASE_TAG=$tag" >> "$GITHUB_ENV"
+          echo "RELEASE_VERSION=$tag" >> "$GITHUB_ENV"
 
       - name: Checkout release staging branch
         run: |
@@ -50,7 +50,7 @@ jobs:
           GH_TOKEN: ${{ secrets.GH_TOKEN }}
         run: |
           pip install requests packaging
-          python .github/scripts/generate_changelog.py -p cellml/libcellml PREV ${{ env.RELEASE_TAG }}
+          python .github/scripts/generate_changelog.py -p cellml/libcellml PREV v${{ env.RELEASE_VERSION }}
           mv changelog_*.rst docs/changelogs/
           python .github/scripts/clean_and_reindex_changelogs.py .
 
@@ -60,5 +60,5 @@ jobs:
           git config user.email "github-actions[bot]@users.noreply.github.com"
 
           git add docs/changelogs/changelog_*.rst docs/changelogs/index.rst docs/index.rst
-          git commit -m "Add changelog for release ${RELEASE_TAG}" || echo "No changes to commit"
+          git commit -m "Add changelog for release ${RELEASE_VERSION}" || echo "No changes to commit"
           git push

.github/workflows/release-prepare.yml

@@ -25,6 +25,11 @@ jobs:
           ref: release
           path: release-repo
 
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ inputs.source_branch }}
+          path: source-repo
+
       - name: Detect active release staging branches (PR-backed)
         id: detect_branch
         env:
@@ -65,32 +70,31 @@ jobs:
           #branch="${active[0]}"
           #echo "release_branch=$branch" >> "$GITHUB_OUTPUT"
 
-      - name: Set GitHub Actions bot identity
+      - name: Set GitHub Actions bot identity (both repos)
         run: |
           cd release-repo
 
           git config user.name "github-actions[bot]"
           git config user.email "github-actions[bot]@users.noreply.github.com"
 
-      - uses: actions/checkout@v6
-        with:
-          ref: ${{ inputs.source_branch }}
-          path: source-repo
+          cd ../source-repo
 
-      - name: Create staging branch
-        run: |
-          cd release-repo
-          git checkout -b ${{ vars.RELEASE_STAGING_BRANCH_STEM }}${{ inputs.version }}
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
 
       - name: Tag source of release
         run: |
           cd source-repo
 
-          git config user.name "github-actions[bot]"
-          git config user.email "github-actions[bot]@users.noreply.github.com"
           git tag -a "source-v${{ inputs.version }}" -m "Source tag for release v${{ inputs.version }}"
           git push origin "source-v${{ inputs.version }}"
 
+      - name: Create staging branch
+        run: |
+          cd release-repo
+
+          git checkout -b ${{ vars.RELEASE_STAGING_BRANCH_STEM }}${{ inputs.version }}
+
       - name: Copy release changes to release repo
         run: |
           rsync -avW --delete --exclude='.git' source-repo/ release-repo/
@@ -105,6 +109,7 @@ jobs:
       - name: Push branch
         run: |
           cd release-repo
+
           git push origin ${{ vars.RELEASE_STAGING_BRANCH_STEM }}${{ inputs.version }}
 
   generate_changelog:

CMakeLists.txt

@@ -21,7 +21,7 @@ endif()
 set(PROJECT_NAME libCellML)
 set(PROJECT_URL https://libcellml.org)
 set(_PROJECT_VERSION 0.7.0)
-set(PROJECT_DEVELOPER_VERSION -rc.4)
+set(PROJECT_DEVELOPER_VERSION )
 project(${PROJECT_NAME} VERSION ${_PROJECT_VERSION} LANGUAGES CXX)
 
 # Set policies that affect the build.

docs/changelogs/changelog_v0.7.0.rst

@@ -0,0 +1,106 @@
+libCellML v0.7.0 Changelog
+==========================
+
+Analyser
+--------
+
+* Improve caching of equivalent variables in analyser model by `@hsorby <https://github.com/hsorby>`_ [`#1389 <https://github.com/cellml/libcellml/pull/1389>`_].
+* Analyser: account for an underconstrained NLA system by `@agarny <https://github.com/agarny>`_ [`#1338 <https://github.com/cellml/libcellml/pull/1338>`_].
+
+Bug
+---
+
+* Fix bug with litre units by `@hsorby <https://github.com/hsorby>`_ [`#1314 <https://github.com/cellml/libcellml/pull/1314>`_].
+* Fix segfault with imports across multiple directories by `@hsorby <https://github.com/hsorby>`_ [`#1304 <https://github.com/cellml/libcellml/pull/1304>`_].
+
+Documentation
+-------------
+
+* Fix warnings when building the documentation with Doxygen by `@hsorby <https://github.com/hsorby>`_ [`#1349 <https://github.com/cellml/libcellml/pull/1349>`_].
+* Updating citation information for libCellML by `@nickerso <https://github.com/nickerso>`_ [`#1361 <https://github.com/cellml/libcellml/pull/1361>`_].
+
+Generator
+---------
+
+* Generator class holds a reference to an analyser model by `@hsorby <https://github.com/hsorby>`_ [`#1439 <https://github.com/cellml/libcellml/pull/1439>`_].
+* Generator: fix a couple of issues with the Python profile by `@agarny <https://github.com/agarny>`_ [`#1376 <https://github.com/cellml/libcellml/pull/1376>`_].
+* Generator profile: fix `computeComputedConstants()`'s signature by `@agarny <https://github.com/agarny>`_ [`#1364 <https://github.com/cellml/libcellml/pull/1364>`_].
+* Add additional overloads to `Generator` class implementationCode and interfaceCode methods by `@hsorby <https://github.com/hsorby>`_ [`#1345 <https://github.com/cellml/libcellml/pull/1345>`_].
+* Add a `GeneratorVariableTracker` class to manage un/tracked variables by `@agarny <https://github.com/agarny>`_ [`#1340 <https://github.com/cellml/libcellml/pull/1340>`_].
+* Allow a constant, a computed constant, or a state variable (but not an algebraic variable) to be used as an initial value by `@agarny <https://github.com/agarny>`_ [`#1325 <https://github.com/cellml/libcellml/pull/1325>`_].
+* Code generator: allow for variables to be tracked/untracked by `@agarny <https://github.com/agarny>`_ [`#1256 <https://github.com/cellml/libcellml/pull/1256>`_].
+* Code generator: use different arrays for constants, computed constants, and algebraic variables by `@agarny <https://github.com/agarny>`_ [`#1247 <https://github.com/cellml/libcellml/pull/1247>`_].
+* Syntax error in generated Python code by `@agarny <https://github.com/agarny>`_ [`#1334 <https://github.com/cellml/libcellml/pull/1334>`_].
+* API: simplify/improve the API for external variables by `@agarny <https://github.com/agarny>`_ [`#1252 <https://github.com/cellml/libcellml/pull/1252>`_].
+
+Infrastructure
+--------------
+
+* macOS: support version 14.0 and later by `@agarny <https://github.com/agarny>`_ [`#1447 <https://github.com/cellml/libcellml/pull/1447>`_].
+* Output unit test failures to CI logs by `@hsorby <https://github.com/hsorby>`_ [`#1441 <https://github.com/cellml/libcellml/pull/1441>`_].
+* Don't push changes to main too early in finalise workflow by `@hsorby <https://github.com/hsorby>`_ [`#1433 <https://github.com/cellml/libcellml/pull/1433>`_].
+* Reset working directory when ccloning passed documentation repositories by `@hsorby <https://github.com/hsorby>`_ [`#1432 <https://github.com/cellml/libcellml/pull/1432>`_].
+* Revert to windows-2022 to avoid issues with windows-2025 by `@hsorby <https://github.com/hsorby>`_ [`#1431 <https://github.com/cellml/libcellml/pull/1431>`_].
+* Try a different approach to setting permissions for make release workflow by `@hsorby <https://github.com/hsorby>`_ [`#1430 <https://github.com/cellml/libcellml/pull/1430>`_].
+* Re-instate final fixes to release process workflow overwritten during testing by `@hsorby <https://github.com/hsorby>`_ [`#1428 <https://github.com/cellml/libcellml/pull/1428>`_].
+* Perform final sanity check before pushing release changes to main by `@hsorby <https://github.com/hsorby>`_ [`#1427 <https://github.com/cellml/libcellml/pull/1427>`_].
+* Correct conditional syntax in finalise release workflow by `@hsorby <https://github.com/hsorby>`_ [`#1426 <https://github.com/cellml/libcellml/pull/1426>`_].
+* Skip user documentation update if the documentation tests failed by `@hsorby <https://github.com/hsorby>`_ [`#1425 <https://github.com/cellml/libcellml/pull/1425>`_].
+* Fix more references to libcellml/website-src by `@hsorby <https://github.com/hsorby>`_ [`#1424 <https://github.com/cellml/libcellml/pull/1424>`_].
+* Fix the way commits for release are pushed to main by `@hsorby <https://github.com/hsorby>`_ [`#1423 <https://github.com/cellml/libcellml/pull/1423>`_].
+* Set default summary if documentation checks returns nothing by `@hsorby <https://github.com/hsorby>`_ [`#1422 <https://github.com/cellml/libcellml/pull/1422>`_].
+* Fix missing installation of ResolveZLIB.cmake file by `@hsorby <https://github.com/hsorby>`_ [`#1421 <https://github.com/cellml/libcellml/pull/1421>`_].
+* Set identity of Git user to github actions bot for tagging release source by `@hsorby <https://github.com/hsorby>`_ [`#1419 <https://github.com/cellml/libcellml/pull/1419>`_].
+* Correctly tag source of release by `@hsorby <https://github.com/hsorby>`_ [`#1418 <https://github.com/cellml/libcellml/pull/1418>`_].
+* Switch to release branch before committing changelog changes by `@hsorby <https://github.com/hsorby>`_ [`#1416 <https://github.com/cellml/libcellml/pull/1416>`_].
+* Remove -v from git tag -a command in release-prepare.yml by `@hsorby <https://github.com/hsorby>`_ [`#1415 <https://github.com/cellml/libcellml/pull/1415>`_].
+* Set a source tag and use that to determine which merge commits to consider by `@hsorby <https://github.com/hsorby>`_ [`#1414 <https://github.com/cellml/libcellml/pull/1414>`_].
+* Tweaks to release process, investigating changelog creation issue by `@hsorby <https://github.com/hsorby>`_ [`#1412 <https://github.com/cellml/libcellml/pull/1412>`_].
+* Adjust finalise release workflow by `@hsorby <https://github.com/hsorby>`_ [`#1411 <https://github.com/cellml/libcellml/pull/1411>`_].
+* Release process fixes by `@hsorby <https://github.com/hsorby>`_ [`#1409 <https://github.com/cellml/libcellml/pull/1409>`_].
+* Add finalise release workflow by `@hsorby <https://github.com/hsorby>`_ [`#1405 <https://github.com/cellml/libcellml/pull/1405>`_].
+* Add make release workflow by `@hsorby <https://github.com/hsorby>`_ [`#1404 <https://github.com/cellml/libcellml/pull/1404>`_].
+* Add check release workflow by `@hsorby <https://github.com/hsorby>`_ [`#1403 <https://github.com/cellml/libcellml/pull/1403>`_].
+* Add GitHub action to prepare a release by `@hsorby <https://github.com/hsorby>`_ [`#1394 <https://github.com/cellml/libcellml/pull/1394>`_].
+* Shift from OpenCMISS dependencies to CMLibs dependencies by `@hsorby <https://github.com/hsorby>`_ [`#1378 <https://github.com/cellml/libcellml/pull/1378>`_].
+* GHA: account for the fact that `macos-13` is about to be retired by `@agarny <https://github.com/agarny>`_ [`#1329 <https://github.com/cellml/libcellml/pull/1329>`_].
+* CMake: cannot use `DEPENDS` with `add_custom_command(TARGET ...)` by `@agarny <https://github.com/agarny>`_ [`#1319 <https://github.com/cellml/libcellml/pull/1319>`_].
+* CI by `@agarny <https://github.com/agarny>`_ [`#1315 <https://github.com/cellml/libcellml/pull/1315>`_].
+
+JavaScript bindings
+-------------------
+
+* JavaScript: account for the fact that our JavaScript bindings use a 32-bit address space by `@agarny <https://github.com/agarny>`_ [`#1384 <https://github.com/cellml/libcellml/pull/1384>`_].
+
+Miscellaneous
+-------------
+
+* Update C++ standard to version 20 by `@agarny <https://github.com/agarny>`_ [`#1390 <https://github.com/cellml/libcellml/pull/1390>`_].
+* Remove all unnecessary headers as guided by Qt Creator on macOS by `@hsorby <https://github.com/hsorby>`_ [`#1346 <https://github.com/cellml/libcellml/pull/1346>`_].
+* Remove second definition of AnalyserModelWeakPtr by `@hsorby <https://github.com/hsorby>`_ [`#1343 <https://github.com/cellml/libcellml/pull/1343>`_].
+
+Python bindings
+---------------
+
+* Add 3.14 to cibuildwheel builds by `@hsorby <https://github.com/hsorby>`_ [`#1444 <https://github.com/cellml/libcellml/pull/1444>`_].
+
+Validation
+----------
+
+* Improve the time taken to validate and analyse large models by `@hsorby <https://github.com/hsorby>`_ [`#1397 <https://github.com/cellml/libcellml/pull/1397>`_].
+
+Contributors
+------------
+
+.. image:: https://avatars.githubusercontent.com/u/778048?v=4
+   :target: https://github.com/hsorby
+   :height: 32
+   :width: 32
+.. image:: https://avatars.githubusercontent.com/u/602265?v=4
+   :target: https://github.com/agarny
+   :height: 32
+   :width: 32
+.. image:: https://avatars.githubusercontent.com/u/811244?v=4
+   :target: https://github.com/nickerso
+   :height: 32
+   :width: 32

docs/changelogs/index.rst

@@ -4,7 +4,7 @@ Changelogs
 
 .. toctree::
 
-   changelog_v0.7.0-rc.4
+   changelog_v0.7.0
    changelog_v0.6.3
    changelog_v0.6.2
    changelog_v0.6.1

docs/index.rst

@@ -39,7 +39,7 @@ Changelogs
 
 .. toctree::
 
-   changelogs/changelog_v0.7.0-rc.4
+   changelogs/changelog_v0.7.0
    changelogs/changelog_v0.6.3
    changelogs/changelog_v0.6.2
    changelogs/changelog_v0.6.1

src/analyser.cpp

@@ -403,8 +403,17 @@ AnalyserInternalVariablePtr Analyser::AnalyserImpl::internalVariable(const Varia
     // Find and return, if there is one, the internal variable associated with
     // the given variable.
 
+    auto rawPtr = reinterpret_cast<uintptr_t>(variable.get());
+    auto rawPtrIt = mInternalVariableMap.find(rawPtr);
+
+    if (rawPtrIt != mInternalVariableMap.end()) {
+        return rawPtrIt->second;
+    }
+
     for (const auto &internalVariable : mInternalVariables) {
         if (mAnalyserModel->areEquivalentVariables(variable, internalVariable->mVariable)) {
+            mInternalVariableMap[rawPtr] = internalVariable;
+
             return internalVariable;
         }
     }
@@ -416,6 +425,8 @@ AnalyserInternalVariablePtr Analyser::AnalyserImpl::internalVariable(const Varia
 
     mInternalVariables.push_back(res);
 
+    mInternalVariableMap[rawPtr] = res;
+
     return res;
 }
 
@@ -2321,6 +2332,7 @@ void Analyser::AnalyserImpl::analyseModel(const ModelPtr &model)
     mAnalyserModel = AnalyserModel::AnalyserModelImpl::create(model);
 
     mInternalVariables.clear();
+    mInternalVariableMap.clear();
     mInternalEquations.clear();
 
     mCiCnUnits.clear();

src/analyser_p.h

@@ -161,6 +161,7 @@ class Analyser::AnalyserImpl: public Logger::LoggerImpl
     AnalyserExternalVariablePtrs mExternalVariables;
 
     AnalyserInternalVariablePtrs mInternalVariables;
+    std::unordered_map<std::uintptr_t, AnalyserInternalVariablePtr> mInternalVariableMap;
     AnalyserInternalEquationPtrs mInternalEquations;
 
     GeneratorProfilePtr mGeneratorProfile = GeneratorProfile::create();