diff --git a/.github/instructions/python-dependencies.instructions.md b/.github/instructions/python-dependencies.instructions.md index 72aeeba58..bed628b70 100644 --- a/.github/instructions/python-dependencies.instructions.md +++ b/.github/instructions/python-dependencies.instructions.md @@ -1,44 +1,43 @@ --- -applyTo: "requirements.txt,conda-environment.yml" +applyTo: "pyproject.toml,conda-environment.yml" --- # Python Dependency Conventions -Applies to [requirements.txt](../../requirements.txt), [conda-environment.yml](../../conda-environment.yml). +[pyproject.toml](../../pyproject.toml), [conda-environment.yml](../../conda-environment.yml). ## Sync Rule -Both files must stay **in sync**: same packages, same pinned versions. Package in one must be in other. +`pyproject.toml` canonical source. `conda-environment.yml` stays synced: same packages, same pinned versions. -Exceptions (document inline with comment if they differ): -- `conda-environment.yml` may split packages (e.g. `plotly[kaleido]` in pip vs. `plotly` + `python-kaleido` in conda) -- `conda-environment.yml` may use `pip:` block for packages not on conda-forge +Exceptions (inline comment if differ): +- `conda-environment.yml` splits packages (e.g. `plotly[kaleido]` in pyproject.toml vs. `plotly` + `python-kaleido` in conda) +- `conda-environment.yml` uses `pip:` block for packages not on conda-forge ## Versioning - Pin all versions — no ranges, no `>=`, no unpinned entries -- `requirements.txt`: `==` (e.g. `pandas==2.2.3`) -- `conda-environment.yml`: `=` (e.g. `pandas=2.2.3`) +- `pyproject.toml`: `==` (e.g. `"pandas==2.3.3"`) +- `conda-environment.yml`: `=` (e.g. `pandas=2.3.3`) -## Adding or Updating +## Updating -- **Ask user before introducing new dependencies** +- **Ask user before adding dependencies** - Update both files when changing version ## Verification -**`requirements.txt`** — venv dry-run from [.github/workflows/internal-check-python-venv-support.yml](../../.github/workflows/internal-check-python-venv-support.yml): +**`pyproject.toml`** — uv sync from [.github/workflows/internal-check-python-uv-support.yml](../../.github/workflows/internal-check-python-uv-support.yml): ```shell -python -m venv .venv -source ./scripts/activatePythonEnvironment.sh -.venv/bin/pip install --dry-run --quiet --requirement requirements.txt -! .venv/bin/pip install --dry-run --requirement requirements.txt 2>/dev/null | grep -q "Would install" +uv sync --frozen +uv lock --check +uv run python -c "import ipykernel, pandas, sklearn, umap, shap, neo4j, plotly, optuna" ``` **`conda-environment.yml`** — via [scripts/activateCondaEnvironment.sh](../../scripts/activateCondaEnvironment.sh): ```shell -source ./scripts/activateCondaEnvironment.sh +PYTHON_PACKAGE_MANAGER=conda source ./scripts/activateCondaEnvironment.sh ``` Fallback (conda directly): diff --git a/.github/instructions/renovate.instructions.md b/.github/instructions/renovate.instructions.md new file mode 100644 index 000000000..9a710a716 --- /dev/null +++ b/.github/instructions/renovate.instructions.md @@ -0,0 +1,64 @@ +--- +applyTo: "renovate.json" +--- +# Renovate Config Conventions + +## Valid JSON + +File must be valid JSON. No trailing commas. Validate with: + +```shell +npx --yes --package renovate -- renovate-config-validator +``` + +## $schema + +Top-level field must have schema reference: + +```json +{ + "$schema": "https://docs.renovatebot.com/renovate-schema.json" +} +``` + +## customManagers + +Each entry requires: + +- `"customType": "regex"` — mandatory for regex managers +- `"description"` — short human-readable string. State what updated, where. + +Example: + +```json +{ + "description": "Update NEO4J_VERSION constant in shell scripts", + "customType": "regex", + "fileMatch": ["^scripts/[^/]*\\.sh$"], + "matchStrings": ["NEO4J_VERSION:-\\\"?(?.*?)\\\""] +} +``` + +## packageRules + +Each entry requires: + +- `"description"` — short string. Clarify rule purpose. + +Example: + +```json +{ + "description": "Keep Python ML libraries in sync", + "matchDatasources": ["pypi"], + "matchPackageNames": ["scikit-**", "umap-learn"], + "groupName": "python-machine-learning-libs" +} +``` + +## Escaping + +Use `\\` in `matchStrings` + `fileMatch`. Single `\` → invalid JSON. + +- `.` → `\\.` +- `"` → `\\\"` diff --git a/.github/prompts/plan-uvAsPrimaryPackageManager.prompt.md b/.github/prompts/plan-uvAsPrimaryPackageManager.prompt.md new file mode 100644 index 000000000..2fd3be776 --- /dev/null +++ b/.github/prompts/plan-uvAsPrimaryPackageManager.prompt.md @@ -0,0 +1,107 @@ +# Plan: uv as Primary Package Manager + +uv becomes the primary (default) Python package manager using `pyproject.toml` + `uv.lock` as the canonical dependency source. Conda remains a supported optional path. venv is removed entirely. All wiring — scripts, workflows, Renovate, docs, and instruction files — is updated accordingly. + +--- + +## Phase 1 — Canonical Dependency Source +1. **Create `pyproject.toml`**: `[project]` section with `requires-python = ">=3.12"`, `dependencies` pinned with `==` (exact versions from `requirements.txt`); `[tool.uv]` for uv settings +2. **Delete `requirements.txt`** — Renovate's `uv` manager takes over version tracking +3. **Fix drift in `conda-environment.yml`**: `pandas=2.2.3` → `2.3.3`; `neo4j==5.28.2` → `6.1.0` in its pip block +4. **Update header comment** in `conda-environment.yml`: "sync to `pyproject.toml`" (not requirements.txt) + +**Verification**: `uv sync` completes cleanly; `uv lock --check` passes. + +## Phase 2 — Activation Scripts *(parallel with Phase 3)* +5. **Create `scripts/activateUvEnvironment.sh`**: skips early if `PYTHON_PACKAGE_MANAGER != 'uv'`; hard-fails if `uv` not found (with install URL); runs `uv sync --frozen`; activates `.venv/bin/activate` (Unix) or `.venv/Scripts/activate` (Windows Git Bash) — cross-platform via `operatingSystemFunctions.sh`; shellcheck-clean, follows [shell-scripts.instructions.md](.github/instructions/shell-scripts.instructions.md) +6. **Delete `scripts/activatePythonEnvironment.sh`** +7. **Modify `scripts/activateCondaEnvironment.sh`**: replace `USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV == 'true'` skip-guard → `PYTHON_PACKAGE_MANAGER != 'conda'`; leave deprecated var in comment + +## Phase 3 — Environment Variables *(parallel with Phase 2)* +8. **Add `PYTHON_PACKAGE_MANAGER`** env var (default: `uv`, valid: `uv` | `conda`) to both new activation scripts +9. **Deprecate `USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV`** — mark in all referencing scripts +10. **Remove `PYTHON_ENVIRONMENT_FILE`** — referenced only by the deleted `activatePythonEnvironment.sh` + +## Phase 4 — Pipeline Script Wiring *(depends on 2 + 3)* +11. **Modify `scripts/reports/compilations/PythonReports.sh`**: replace `source activatePythonEnvironment.sh` → `source activateUvEnvironment.sh`; keep `activateCondaEnvironment.sh` call; update comment +12. **Modify `scripts/checkCompatibility.sh`**: replace `oneOf "conda" "venv"` → `oneOf "uv" "conda"`; replace `checkOptionalCommand "virtualenv"` → `checkOptionalCommand "uv"` (with astral.sh URL); remove `python`/`pip` as required commands (uv manages its own Python) + +## Phase 5 — Workflows *(depends on 2 + 3 + 4)* +13. **Rename** `internal-check-python-venv-support.yml` → `internal-check-python-uv-support.yml`: install uv via `astral-sh/setup-uv`; `uv sync --frozen`; verify package imports; trigger paths: `pyproject.toml`, `uv.lock`, `scripts/activateUvEnvironment.sh` +14. **Create** `.github/workflows/internal-check-conda-support.yml`: setup-miniconda + `conda-environment.yml`; verify activation + imports; trigger paths: `conda-environment.yml`, `scripts/activateCondaEnvironment.sh` +15. **Modify `public-analyze-code-graph.yml`** (public API — no breaking changes): + - Add `python-package-manager` input: `type: string`, `default: 'uv'`, `required: false`, self-contained description for external users + - Update `use-venv_virtual_python_environment` description: "Deprecated. Use `python-package-manager` instead." + - Add uv setup step (conditional `inputs.python-package-manager != 'conda'`) using `astral-sh/setup-uv` + - Keep conda setup step (conditional `inputs.python-package-manager == 'conda'`) + - Pass `PYTHON_PACKAGE_MANAGER: ${{ inputs.python-package-manager }}` to the analysis env + - ⚠️ **Behavior change**: callers relying on conda being the effective default must now explicitly pass `python-package-manager: 'conda'` +16. **Modify `internal-java-code-analysis.yml`**: remove `!requirements.txt` override from `paths-ignore` (2 occurrences); no other changes — inherits uv default +17. **Modify `internal-typescript-code-analysis.yml`**: same `!requirements.txt` removal + +## Phase 6 — Renovate *(parallel with Phase 5)* +18. **Modify `renovate.json`**: add `"uv"` to `matchManagers` in the "Only use stable versions" packageRule; remove `"pip_requirements"` from the same list; Renovate's `uv` manager auto-discovers `pyproject.toml` + `uv.lock` + - 🔘 **Decision point**: enable the currently-disabled conda customManagers? (change `fileMatch` from `conda-environment-temporarily-disabled.yml` → `conda-environment.yml`) + +## Phase 7 — Documentation *(depends on all above)* +19. **`README.md`**: update Python prerequisites (uv primary, conda optional) +20. **`COMMANDS.md`**: add uv setup commands; keep conda manual setup section +21. **`ENVIRONMENT_VARIABLES.md`**: add `PYTHON_PACKAGE_MANAGER`, deprecate `USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV`, remove `PYTHON_ENVIRONMENT_FILE` +22. **Regenerate `SCRIPTS.md`** (run generation script after all script changes) +23. **`AGENTS.md`, `CLAUDE.md`, `.github/copilot-instructions.md`**: update instruction table row for `python-dependencies.instructions.md` (applyTo now covers `pyproject.toml`) + +## Phase 8 — Instruction Files *(depends on all above)* +24. **Modify `.github/instructions/python-dependencies.instructions.md`**: update `applyTo` to `pyproject.toml,conda-environment.yml`; update sync rule (`pyproject.toml` is canonical); update verification to `uv sync --check` / `uv lock --check` + +--- + +## Summary Table + +| File | Change | +|------|--------| +| `pyproject.toml` | **NEW** — canonical dep source | +| `requirements.txt` | **DELETED** | +| `conda-environment.yml` | drift fix + header comment update | +| `scripts/activateUvEnvironment.sh` | **NEW** | +| `scripts/activatePythonEnvironment.sh` | **DELETED** | +| `scripts/activateCondaEnvironment.sh` | gate on `PYTHON_PACKAGE_MANAGER` | +| `scripts/reports/compilations/PythonReports.sh` | swap activation script | +| `scripts/checkCompatibility.sh` | uv/conda check, remove pip/python | +| `.github/workflows/internal-check-python-venv-support.yml` | **RENAMED** → uv-support.yml | +| `.github/workflows/internal-check-conda-support.yml` | **NEW** | +| `.github/workflows/public-analyze-code-graph.yml` | add `python-package-manager` param | +| `.github/workflows/internal-java-code-analysis.yml` | remove `!requirements.txt` exception | +| `.github/workflows/internal-typescript-code-analysis.yml` | remove `!requirements.txt` exception | +| `renovate.json` | add `uv` manager, remove `pip_requirements` | +| `ENVIRONMENT_VARIABLES.md` | new var, deprecated var, removed var | +| `SCRIPTS.md` | regenerated | +| `README.md`, `COMMANDS.md` | uv setup docs | +| `AGENTS.md`, `CLAUDE.md`, `.github/copilot-instructions.md` | instruction table update | +| `.github/instructions/python-dependencies.instructions.md` | applyTo + sync rule + verification | + +## Verification Checklist +1. `uv sync --frozen` completes cleanly from project root +2. `uv lock --check` — lockfile is consistent with `pyproject.toml` +3. `uv run python -c "import ipykernel, pandas, sklearn, umap, shap, neo4j, plotly, optuna"` — all imports succeed +4. `shellcheck scripts/activateUvEnvironment.sh scripts/activateCondaEnvironment.sh` — no warnings +5. `npx --yes markdown-link-check --quiet --progress --config=markdown-lint-check-config.json README.md COMMANDS.md ENVIRONMENT_VARIABLES.md` — no broken links +6. CI: `internal-check-python-uv-support.yml` passes +7. CI: `internal-check-conda-support.yml` passes +8. CI: `public-analyze-code-graph.yml` smoke-tested with default (uv) and with `python-package-manager: conda` + +## Renovate Decision +- Should Renovate's conda customManagers be re-enabled now that `conda-environment.yml` is officially the conda canonical file? Currently disabled on purpose. Enabling makes Renovate auto-update conda packages but the custom matchers only cover conda packages (not the nested pip block). Answer: Yes, but it is fine when conda versions diverge from pyproject.toml since conda is now explicitly optional and secondary. Therefore, enable it and change it so that it only matches `conda-environment.yml` and only takes conda package updates into account (ignore pip block). + +## Key Decisions Made +- **Canonical source**: `pyproject.toml` + `uv.lock` +- **`requirements.txt`**: deleted entirely; Renovate `uv` manager handles updates +- **`conda-environment.yml`**: kept; synced to `pyproject.toml` (not deleted) +- **Drift fix** (in this PR): `pandas=2.3.3`, `neo4j==6.1.0` (use requirements.txt versions as truth) +- **Script**: new `activateUvEnvironment.sh`; delete `activatePythonEnvironment.sh` +- **Env var**: new `PYTHON_PACKAGE_MANAGER` (default: `uv`); `USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV` deprecated +- **Public workflow**: add `python-package-manager` string param (default `'uv'`); keep old param deprecated-but-present + - **Behavior change flag**: callers relying on old conda default (VENV=false) now get uv. Must set `python-package-manager: 'conda'` explicitly. +- **CI**: uv = primary (existing internal workflows), conda = new dedicated check workflow +- **Renovate**: enable `uv` manager; remove/disable `pip_requirements` since no more requirements.txt +- **Windows Git Bash / WSL**: supported in `activateUvEnvironment.sh` +- **Jupyter**: `ipykernel==7.2.0` already in both files — no changes needed diff --git a/.github/workflows/internal-check-conda-support.yml b/.github/workflows/internal-check-conda-support.yml new file mode 100644 index 000000000..e977d7efe --- /dev/null +++ b/.github/workflows/internal-check-conda-support.yml @@ -0,0 +1,49 @@ +name: Check Python Conda environment + +on: + pull_request: + branches: + - main + # Only watch changes related to the Conda environment + paths: + - 'conda-environment.yml' + - 'scripts/activateCondaEnvironment.sh' + - '.github/workflows/internal-check-conda-support.yml' # or when this file changed + +jobs: + check-conda-environment: + runs-on: ubuntu-22.04 + strategy: + matrix: + include: + - python: 3.12 + miniforge: 24.9.0-0 + + steps: + - name: Checkout GIT Repository + uses: actions/checkout@v6 + + - name: (Python Setup) Use version ${{ matrix.python }} with Conda package manager Miniforge + uses: conda-incubator/setup-miniconda@v3 + with: + python-version: ${{ matrix.python }} + miniforge-version: ${{ matrix.miniforge }} + activate-environment: codegraph + environment-file: ./conda-environment.yml + auto-activate-base: false + show-channel-urls: true + + - name: (Python Setup) Conda environment info + shell: bash -el {0} + run: | + conda info + conda list + + - name: Activate Conda environment and verify required packages are importable + env: + PYTHON_PACKAGE_MANAGER: "conda" + PREPARE_CONDA_ENVIRONMENT: "false" # Already prepared above + shell: bash -el {0} + run: | + source ./scripts/activateCondaEnvironment.sh + python -c "import ipykernel, pandas, sklearn, umap, shap, neo4j, plotly, optuna" diff --git a/.github/workflows/internal-check-python-uv-support.yml b/.github/workflows/internal-check-python-uv-support.yml new file mode 100644 index 000000000..b41a4505c --- /dev/null +++ b/.github/workflows/internal-check-python-uv-support.yml @@ -0,0 +1,38 @@ +name: Check Python uv environment + +on: + pull_request: + branches: + - main + # Only watch changes related to Python uv environment + paths: + - 'pyproject.toml' + - 'uv.lock' + - 'scripts/activateUvEnvironment.sh' + - '.github/workflows/internal-check-python-uv-support.yml' # or when this file changed + +jobs: + check-python-uv-environment: + runs-on: ubuntu-22.04 + strategy: + matrix: + include: + - python: 3.12 + + steps: + - name: Checkout GIT Repository + uses: actions/checkout@v6 + + - name: (uv Setup) Install uv + uses: astral-sh/setup-uv@v6 + with: + python-version: ${{ matrix.python }} + + - name: (uv Setup) Sync dependencies from lockfile + run: uv sync --frozen + + - name: Verify activation script and required packages + run: | + source ./scripts/activateUvEnvironment.sh + python -c "import ipykernel, pandas, sklearn, umap, shap, neo4j, plotly, optuna" + echo "✓ Activation script and imports successful" diff --git a/.github/workflows/internal-check-python-venv-support.yml b/.github/workflows/internal-check-python-venv-support.yml deleted file mode 100644 index 3ff551e41..000000000 --- a/.github/workflows/internal-check-python-venv-support.yml +++ /dev/null @@ -1,48 +0,0 @@ -name: Check Python venv virtual environment - -on: - pull_request: - branches: - - main - # Only watch changes related to Python virtual environment venv - paths: - - 'requirements.txt' - - 'scripts/activatePythonEnvironment.sh' - - '.github/workflows/internal-check-python-venv-support.yml' # or when this file changed - -jobs: - check-python-venv-environment: - runs-on: ubuntu-22.04 - strategy: - matrix: - include: - - python: 3.12 - - steps: - - name: Checkout GIT Repository - uses: actions/checkout@v6 - - - name: (Python Setup) Use version ${{ matrix.python }} with venv environment management module - uses: actions/setup-python@v6 - with: - python-version: ${{ matrix.python }} - cache: 'pip' - - - name: Activate virtual environment using venv and check if the required packages were installed - env: - USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV: "true" - # 1. Run the script under test to create, activate and install the virtual environment - # 2. Run pip install for the current environment in dry-mode with full output first to get all infos and fail on missing packages. - # 3a. The leading exclamation mark tells the shell to invert the returned exit code. - # Failing because "Would install" is missing leads to a successful execution. - # 3b. Run pip install for the current environment in dry-run mode without installing or resolving dependencies - # 3c. Suppress all pip output (stderr) - # 3d. Check if pip would install anything using grep - # 3e. If there are missing dependencies and the environment is incomplete, - # fail with code 1 (indicates all requirements already satisfied) - # - # Output installed dependencies for troubleshooting purposes:.venv/bin/pip freeze - run: | - source ./scripts/activatePythonEnvironment.sh - .venv/bin/pip install --dry-run --quiet --requirement requirements.txt - ! .venv/bin/pip install --dry-run --requirement requirements.txt 2>/dev/null | grep -q "Would install" \ No newline at end of file diff --git a/.github/workflows/internal-java-code-analysis.yml b/.github/workflows/internal-java-code-analysis.yml index 28754df9d..c79c64356 100644 --- a/.github/workflows/internal-java-code-analysis.yml +++ b/.github/workflows/internal-java-code-analysis.yml @@ -8,7 +8,6 @@ on: paths-ignore: - '**/*.md' - '**/*.txt' - - '!requirements.txt' - '**/*.css' - '**/*.html' - '**/*.js' @@ -27,7 +26,6 @@ on: paths-ignore: - '**/*.md' - '**/*.txt' - - '!requirements.txt' - '**/*.css' - '**/*.html' - '**/*.js' diff --git a/.github/workflows/internal-typescript-code-analysis.yml b/.github/workflows/internal-typescript-code-analysis.yml index 4a60b430c..0d3aaa665 100644 --- a/.github/workflows/internal-typescript-code-analysis.yml +++ b/.github/workflows/internal-typescript-code-analysis.yml @@ -8,7 +8,6 @@ on: paths-ignore: - '**/*.md' - '**/*.txt' - - '!requirements.txt' - '**/*.css' - '**/*.html' - '**/*.js' @@ -27,7 +26,6 @@ on: paths-ignore: - '**/*.md' - '**/*.txt' - - '!requirements.txt' - '**/*.css' - '**/*.html' - '**/*.js' diff --git a/.github/workflows/public-analyze-code-graph.yml b/.github/workflows/public-analyze-code-graph.yml index bc9d76d96..0c29e99e2 100644 --- a/.github/workflows/public-analyze-code-graph.yml +++ b/.github/workflows/public-analyze-code-graph.yml @@ -119,10 +119,21 @@ on: default: 5 use-venv_virtual_python_environment: description: > - Use venv for virtual Python environments instead of Conda ("true") or not ("false", default). + Deprecated and ignored. venv support has been removed in favor of uv (default) or conda. + Use the `python-package-manager` input to select either "uv" or "conda". required: false type: string default: 'false' + python-package-manager: + description: > + Python package manager to use for Python reports. + Options: "uv" (default) or "conda". + "uv" uses pyproject.toml + uv.lock for a reproducible virtual environment. + "conda" uses conda-environment.yml and requires Conda (e.g. Miniforge) to be available. + Callers previously relying on the conda default via use-venv_virtual_python_environment=false must now explicitly set python-package-manager: 'conda'. + required: false + type: string + default: 'uv' outputs: uploaded-analysis-results: description: > @@ -152,6 +163,10 @@ jobs: echo "The analysis-name '${{ inputs.analysis-name }}' contains invalid characters. Only alphanumeric characters, dots (.), underscores (_) and hyphens (-) are allowed." exit 1 fi + - name: Warn about deprecated use-venv_virtual_python_environment parameter + if: inputs.use-venv_virtual_python_environment == 'true' + run: | + echo "::warning::The 'use-venv_virtual_python_environment' input is deprecated. Use 'python-package-manager: uv' instead. This warning will become an error in a future release." - name: Assemble ENVIRONMENT_INFO run: echo "ENVIRONMENT_INFO=java-${{ matrix.java }}-python-${{ matrix.python }}-miniforge-${{ matrix.miniforge }}" >> $GITHUB_ENV @@ -170,8 +185,14 @@ jobs: java-version: ${{ matrix.java }} # Python setup is always performed here since this is a reusable workflow. + - name: (Python Setup) Install uv + if: inputs.python-package-manager != 'conda' + uses: astral-sh/setup-uv@v6 + with: + python-version: ${{ matrix.python }} + - name: (Python Setup) Use version ${{ matrix.python }} with Conda package manager Miniforge - if: inputs.use-venv_virtual_python_environment == 'false' + if: inputs.python-package-manager == 'conda' id: prepare-conda-environment uses: conda-incubator/setup-miniconda@fc2d68f6413eb2d87b895e92f8584b5b94a10167 # v3 with: @@ -190,7 +211,7 @@ jobs: cache: 'pip' - name: (Python Setup) Conda environment info - if: inputs.use-venv_virtual_python_environment == 'false' + if: inputs.python-package-manager == 'conda' shell: bash -el {0} run: | conda info @@ -293,7 +314,8 @@ jobs: NEO4J_INITIAL_PASSWORD: ${{ steps.generate-neo4j-initial-password.outputs.neo4j-initial-password }} IMPORT_GIT_LOG_DATA_IF_SOURCE_IS_PRESENT: "" # Options: "none", "aggregated", "full". default = "plugin" or "" PREPARE_CONDA_ENVIRONMENT: "false" # Had already been done in step with id "prepare-conda-environment". - USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV: ${{ inputs.use-venv_virtual_python_environment }} + PYTHON_PACKAGE_MANAGER: ${{ inputs.python-package-manager }} + USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV: ${{ inputs.use-venv_virtual_python_environment }} # Deprecated: use PYTHON_PACKAGE_MANAGER instead. run: | TYPESCRIPT_SCAN_HEAP_MEMORY=${{ inputs.typescript-scan-heap-memory }} ./../../scripts/analysis/analyze.sh ${{ env.domainAnalysisArgument }}${{ env.excludeDomainArgument }}${{ inputs.analysis-arguments }} diff --git a/AGENTS.md b/AGENTS.md index 06eb124bd..17f6b528c 100644 --- a/AGENTS.md +++ b/AGENTS.md @@ -83,10 +83,11 @@ Instruction files auto-applied per file type: | `*.sh` | [.github/instructions/shell-scripts.instructions.md](./.github/instructions/shell-scripts.instructions.md) | | `*.py`, `*.ipynb` | [.github/instructions/python.instructions.md](./.github/instructions/python.instructions.md) | | `*.cypher` | [.github/instructions/cypher-queries.instructions.md](./.github/instructions/cypher-queries.instructions.md) | -| `requirements.txt`, `conda-environment.yml` | [.github/instructions/python-dependencies.instructions.md](./.github/instructions/python-dependencies.instructions.md) | +| `pyproject.toml`, `conda-environment.yml` | [.github/instructions/python-dependencies.instructions.md](./.github/instructions/python-dependencies.instructions.md) | | `CYPHER.md`, `SCRIPTS.md`, `ENVIRONMENT_VARIABLES.md` | [.github/instructions/generated-reference-docs.instructions.md](./.github/instructions/generated-reference-docs.instructions.md) | | `.github/skills/`, `.github/instructions/`, `AGENTS.md` | [.github/instructions/agent-files.instructions.md](./.github/instructions/agent-files.instructions.md) | | `.github/workflows/*.yml` | [.github/instructions/github-workflows.instructions.md](./.github/instructions/github-workflows.instructions.md) | +| `renovate.json` | [.github/instructions/renovate.instructions.md](./.github/instructions/renovate.instructions.md) | --- diff --git a/COMMANDS.md b/COMMANDS.md index a8f7be0c2..af6782fa4 100644 --- a/COMMANDS.md +++ b/COMMANDS.md @@ -211,6 +211,35 @@ The manual setup is only documented for completeness. It isn't needed since the If any of the script are not allowed to be executed use `chmod +x ./scripts/` followed by the script file name to grant execution. +### Setup Python Environment with uv (default) + +[uv](https://docs.astral.sh/uv/) is the default Python package manager. Install it once: + +```shell +curl -LsSf https://astral.sh/uv/install.sh | sh +``` + +Then sync all dependencies from `pyproject.toml` into a local `.venv`: + +```shell +uv sync --frozen +``` + +To verify the lockfile is consistent with `pyproject.toml`: + +```shell +uv lock --check +``` + +### Setup Python Environment with Conda (optional) + +Set `PYTHON_PACKAGE_MANAGER=conda` to use Conda instead of uv. Create and activate the environment manually: + +```shell +conda env update --file conda-environment.yml --prune +conda activate codegraph +``` + ### Setup Neo4j Graph Database Use [setupNeo4j.sh](./domains/neo4j-management/setupNeo4j.sh) to download [Neo4j](https://neo4j.com/download-center) and install the plugins [APOC](https://neo4j.com/labs/apoc/4.4) and [Graph Data Science](https://neo4j.com/product/graph-data-science). @@ -395,6 +424,8 @@ Use [stopNeo4j.sh](./domains/neo4j-management/stopNeo4j.sh) to stop the locally ## References +- [uv - Python package manager](https://docs.astral.sh/uv/) +- [uv - Installation](https://docs.astral.sh/uv/getting-started/installation/) - [Conda](https://conda.io) - [jQAssistant](https://jqassistant.github.io/jqassistant/current) - [Bite-Sized Neo4j for Data Scientists](https://neo4j.com/video/bite-sized-neo4j-for-data-scientists) diff --git a/README.md b/README.md index e527e66dd..9bda99373 100644 --- a/README.md +++ b/README.md @@ -108,14 +108,9 @@ Run [scripts/checkCompatibility.sh](./scripts/checkCompatibility.sh) to check if ### Additional Prerequisites for Python - Python is required for Python reports. -- Either [Conda](https://docs.conda.io) or Python's build-in module [venv](https://docs.python.org/3/library/venv.html) a required as environment manager. -- For Conda, use for example [Miniconda](https://docs.conda.io/projects/miniconda/en/latest) or [Anaconda](https://www.anaconda.com/download)(Recommended for Windows). -- To use venv, no additional installation is needed. For that the environment variable `USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV` needs to be set to `'true'`. - -### Additional Prerequisites for Windows - -- Add this line to your `~/.bashrc` file if you are using Anaconda3: `/c/ProgramData/Anaconda3/etc/profile.d/conda.sh`. Try to find a similar script for other conda package managers or versions. -- Run `conda init` in the git bash opened as administrator. Running it in normal mode usually leads to an error message. +- [uv](https://docs.astral.sh/uv/) is the primary Python package manager (default). Install from [https://docs.astral.sh/uv/getting-started/installation/](https://docs.astral.sh/uv/getting-started/installation/). +- [Conda](https://docs.conda.io) is a supported optional path. Use for example [Miniconda](https://docs.conda.io/projects/miniconda/en/latest) or [Anaconda](https://www.anaconda.com/download) (Recommended for Windows). Set `PYTHON_PACKAGE_MANAGER=conda` to activate. +- For Conda on Windows, add this line to your `~/.bashrc`: `/c/ProgramData/Anaconda3/etc/profile.d/conda.sh`. Run `conda init` in Git Bash as administrator. ### Additional Prerequisites for analyzing Typescript @@ -145,8 +140,8 @@ The [Code Structure Analysis Pipeline](./.github/workflows/internal-java-code-an - Use [GitHub Actions](https://docs.github.com/de/actions) Linux Runner - [Checkout GIT Repository](https://github.com/actions/checkout) - [Setup Java](https://github.com/actions/setup-java) -- [Setup Python with Conda](https://github.com/conda-incubator/setup-miniconda) package manager [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge) -- [Setup Python with venv](https://docs.python.org/3/library/venv.html) +- [Setup uv](https://github.com/astral-sh/setup-uv) — Primary Python package manager +- [Setup Python with Conda](https://github.com/conda-incubator/setup-miniconda) package manager [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge) — Optional alternative - Download artifacts and optionally source code that contain the code to be analyzed [scripts/downloader](./scripts/downloader) - Setup [Neo4j](https://neo4j.com) Graph Database ([analysis.sh](./scripts/analysis/analyze.sh)) - Setup [jQAssistant](https://jqassistant.github.io/jqassistant/current) for Java and [Typescript](https://github.com/jqassistant-plugin/jqassistant-typescript-plugin) analysis ([analysis.sh](./scripts/analysis/analyze.sh)) diff --git a/conda-environment.yml b/conda-environment.yml index 64e8cc2fe..cb9f0bf6f 100644 --- a/conda-environment.yml +++ b/conda-environment.yml @@ -1,4 +1,4 @@ -# NOTE: Keep this file in sync with requirements.txt +# NOTE: Keep this file in sync with pyproject.toml name: codegraph channels: - conda-forge/label/python_rc # Needed on Mac since Python >= 3.12 @@ -7,9 +7,10 @@ channels: dependencies: - python=3.12.9 - _python_rc=1 # Needed on Mac since Python >= 3.12 + - ipykernel=7.2.0 - matplotlib=3.10.8 - numpy=2.2.5 - - pandas=2.2.3 + - pandas=2.3.3 - pip=26.0.1 - setuptools=80.10.2 # opentsne uses sklearn.base uses joblib uses distutils missing in Python >= 12 (TODO use native openTSNE?) - wordcloud=1.9.6 @@ -22,4 +23,4 @@ dependencies: - umap-learn=0.5.11 # to visualize node embeddings in 2D (UMAP dimensionality reduction) - shap=0.50.0 - pip: - - neo4j==5.28.2 + - neo4j==6.1.0 diff --git a/domains/anomaly-detection/treemapVisualizations.py b/domains/anomaly-detection/treemapVisualizations.py index 6d38b17cd..a14440fef 100755 --- a/domains/anomaly-detection/treemapVisualizations.py +++ b/domains/anomaly-detection/treemapVisualizations.py @@ -166,6 +166,12 @@ def query_cypher_to_data_frame(query: LiteralString, parameters: Optional[Dict[s # Ignore kaleido logging noise when writing images logging.getLogger("kaleido").setLevel(logging.WARNING) + +def plotly_values(data: pd.Series | pd.DataFrame) -> list: + """Returns pandas column(s) as a plain Python list for Plotly/orjson serialization.""" + return data.to_numpy().tolist() + + def get_plotly_figure_write_image_settings(name: str, path: str): """ Returns the settings for the plotly figure write_image method @@ -187,10 +193,10 @@ def create_treemap_settings(data_frame: pd.DataFrame, element_path_column: str = return :plotly_graph_objects.Treemap : The prepared Plotly Treemap """ return plotly_graph_objects.Treemap( - labels=data_frame[element_name_column], - parents=data_frame['directoryParentPath'], - ids=data_frame[element_path_column], - customdata=data_frame[['fileCount', 'absoluteAnomalyScore', 'normalizedBridgeRank', 'normalizedOutlierRank', 'elementPath']], + labels=plotly_values(data_frame[element_name_column]), + parents=plotly_values(data_frame['directoryParentPath']), + ids=plotly_values(data_frame[element_path_column]), + customdata=plotly_values(data_frame[['fileCount', 'absoluteAnomalyScore', 'normalizedBridgeRank', 'normalizedOutlierRank', 'elementPath']]), hovertemplate='%{label}
Highlighted anomalies: %{customdata[0]}
Anomaly Score: %{customdata[1]:.4f}
Bridge: %{customdata[2]}, Outlier: %{customdata[3]}
Path: %{customdata[4]}', maxdepth=-1, root_color="lightgrey", @@ -530,7 +536,7 @@ def query_data() -> pd.DataFrame: create_treemap_settings(anomaly_file_paths), marker=dict( **plotly_treemap_marker_base_color_scale, - colors=anomaly_file_paths['absoluteAnomalyScore'], + colors=plotly_values(anomaly_file_paths['absoluteAnomalyScore']), colorbar={"title": "score"}, ), )) diff --git a/domains/archetypes/treemapVisualizations.py b/domains/archetypes/treemapVisualizations.py index 9ea6abf40..eded89626 100755 --- a/domains/archetypes/treemapVisualizations.py +++ b/domains/archetypes/treemapVisualizations.py @@ -156,6 +156,12 @@ def query_cypher_to_data_frame(query: LiteralString, parameters: Optional[Dict[s # Ignore kaleido logging noise when writing images logging.getLogger("kaleido").setLevel(logging.WARNING) + +def plotly_values(data: pd.Series | pd.DataFrame) -> list: + """Returns pandas column(s) as a plain Python list for Plotly/orjson serialization.""" + return data.to_numpy().tolist() + + def get_plotly_figure_write_image_settings(name: str, path: str): return { "file": path + "/" + name + "." + image_rendering_settings['format'], @@ -167,10 +173,10 @@ def get_plotly_figure_write_image_settings(name: str, path: str): def create_treemap_settings(data_frame: pd.DataFrame, element_path_column: str = 'elementPath', element_name_column: str = "elementName") -> plotly_graph_objects.Treemap: return plotly_graph_objects.Treemap( - labels=data_frame[element_name_column], - parents=data_frame['directoryParentPath'], - ids=data_frame[element_path_column], - customdata=data_frame[['fileCount', 'normalizedAuthorityRank', 'normalizedBottleneckRank', 'normalizedHubRank', 'elementPath']], + labels=plotly_values(data_frame[element_name_column]), + parents=plotly_values(data_frame['directoryParentPath']), + ids=plotly_values(data_frame[element_path_column]), + customdata=plotly_values(data_frame[['fileCount', 'normalizedAuthorityRank', 'normalizedBottleneckRank', 'normalizedHubRank', 'elementPath']]), hovertemplate='%{label}
Highlighted archetypes: %{customdata[0]}
Authority: %{customdata[1]}, Bottleneck: %{customdata[2]}, Hub: %{customdata[3]}
Path: %{customdata[4]}', maxdepth=-1, root_color="lightgrey", diff --git a/domains/git-history/gitHistoryCharts.py b/domains/git-history/gitHistoryCharts.py index d26876e6b..3cf338a13 100644 --- a/domains/git-history/gitHistoryCharts.py +++ b/domains/git-history/gitHistoryCharts.py @@ -36,6 +36,13 @@ SCRIPT_NAME = "gitHistoryCharts" + +# ── Plotly serialization ────────────────────────────────────────────────────── + +def plotly_values(data: pd.Series | pd.DataFrame) -> list: + """Returns pandas column(s) as a plain Python list for Plotly/orjson serialization.""" + return data.to_numpy().tolist() + # ── Plotly layout constants ─────────────────────────────────────────────────── PLOTLY_MAIN_LAYOUT_BASE_SETTINGS: dict[str, Any] = dict( @@ -337,11 +344,11 @@ def prepare_directory_commit_statistics(commit_statistics_data: pd.DataFrame) -> def create_treemap_commit_statistics_settings(data_frame: pd.DataFrame) -> plotly_graph_objects.Treemap: """Creates a Plotly Treemap with the given settings and data frame.""" - return plotly_graph_objects.Treemap( - labels=data_frame["directoryName"], - parents=data_frame["directoryParentPath"], - ids=data_frame["directoryPath"], - customdata=data_frame[ + params = dict( + labels=plotly_values(data_frame["directoryName"]), + parents=plotly_values(data_frame["directoryParentPath"]), + ids=plotly_values(data_frame["directoryPath"]), + customdata=plotly_values(data_frame[ [ "fileCount", "mostFrequentFileExtension", @@ -357,7 +364,7 @@ def create_treemap_commit_statistics_settings(data_frame: pd.DataFrame) -> plotl "daysSinceLastModification", "directoryPath", ] - ], + ]), hovertemplate=( "%{label}
" "Files: %{customdata[0]} (%{customdata[1]})
" @@ -372,6 +379,7 @@ def create_treemap_commit_statistics_settings(data_frame: pd.DataFrame) -> plotl root_color="lightgrey", marker=dict(**PLOTLY_TREEMAP_MARKER_BASE_STYLE), ) + return plotly_graph_objects.Treemap(**params) def create_rank_colorbar_for_graph_objects_treemap_marker(data_frame: pd.DataFrame, name_column: str, rank_column: str) -> dict: @@ -379,13 +387,13 @@ def create_rank_colorbar_for_graph_objects_treemap_marker(data_frame: pd.DataFra inverse_ranked = data_frame[rank_column].max() + 1 - data_frame[rank_column] return dict( cornerradius=5, - colors=inverse_ranked, + colors=plotly_values(inverse_ranked), colorscale=plotly_colors.qualitative.G10, colorbar=dict( title="Rank", tickmode="array", - ticktext=data_frame[name_column], - tickvals=inverse_ranked, + ticktext=plotly_values(data_frame[name_column]), + tickvals=plotly_values(inverse_ranked), tickfont_size=10, ), ) @@ -410,7 +418,7 @@ def generate_directory_commit_statistic_treemaps( # 1. Number of files per directory figure = plotly_graph_objects.Figure(plotly_graph_objects.Treemap( create_treemap_commit_statistics_settings(git_files_with_commit_statistics), - values=git_files_with_commit_statistics["fileCount"], + values=plotly_values(git_files_with_commit_statistics["fileCount"]), )) figure.update_layout(**PLOTLY_MAIN_LAYOUT_BASE_SETTINGS, title="Directories and their file count") write_image_and_log(figure, report_directory, "NumberOfFilesPerDirectory", verbose) @@ -437,7 +445,7 @@ def generate_directory_commit_statistic_treemaps( create_treemap_commit_statistics_settings(git_commit_count_per_directory), marker=dict( **PLOTLY_TREEMAP_MARKER_BASE_COLORSCALE, - colors=git_commit_count_per_directory["commitCount_limited"], + colors=plotly_values(git_commit_count_per_directory["commitCount_limited"]), colorbar=dict(title="Commits"), ), )) @@ -450,7 +458,7 @@ def generate_directory_commit_statistic_treemaps( create_treemap_commit_statistics_settings(git_commit_authors_per_directory), marker=dict( **PLOTLY_TREEMAP_MARKER_BASE_COLORSCALE, - colors=git_commit_authors_per_directory["authorCount_limited"], + colors=plotly_values(git_commit_authors_per_directory["authorCount_limited"]), colorbar=dict(title="Authors"), ), )) @@ -459,13 +467,13 @@ def generate_directory_commit_statistic_treemaps( # 5. Directories with very few different authors (low bus-factor, focus = few authors) git_commit_authors_per_directory_low_focus = add_quantile_limited_column(git_files_with_commit_statistics, "authorCount", 0.33) - author_count_top_limit = git_commit_authors_per_directory_low_focus["authorCount_limited"].max().astype(int).astype(str) + author_count_top_limit = str(int(git_commit_authors_per_directory_low_focus["authorCount_limited"].max())) author_count_top_limit_label_alias = {author_count_top_limit: author_count_top_limit + " or more"} figure = plotly_graph_objects.Figure(plotly_graph_objects.Treemap( create_treemap_commit_statistics_settings(git_commit_authors_per_directory_low_focus), marker=dict( **PLOTLY_TREEMAP_MARKER_BASE_COLORSCALE, - colors=git_commit_authors_per_directory_low_focus["authorCount_limited"], + colors=plotly_values(git_commit_authors_per_directory_low_focus["authorCount_limited"]), colorbar=dict( title="Authors", tickmode="auto", @@ -518,7 +526,7 @@ def generate_directory_commit_statistic_treemaps( create_treemap_commit_statistics_settings(git_commit_days_since_last_commit_per_directory), marker=dict( **PLOTLY_TREEMAP_MARKER_BASE_COLORSCALE, - colors=git_commit_days_since_last_commit_per_directory["daysSinceLastCommit_limited"], + colors=plotly_values(git_commit_days_since_last_commit_per_directory["daysSinceLastCommit_limited"]), colorbar=dict(title="Days"), ), )) @@ -531,7 +539,7 @@ def generate_directory_commit_statistic_treemaps( create_treemap_commit_statistics_settings(git_commit_days_since_last_commit_per_directory), marker=dict( **PLOTLY_TREEMAP_MARKER_BASE_COLORSCALE, - colors=git_commit_days_since_last_commit_per_directory["daysSinceLastCommit_rank"], + colors=plotly_values(git_commit_days_since_last_commit_per_directory["daysSinceLastCommit_rank"]), colorbar=dict(title="Rank"), ), )) @@ -544,7 +552,7 @@ def generate_directory_commit_statistic_treemaps( create_treemap_commit_statistics_settings(git_commit_days_since_last_file_creation_per_directory), marker=dict( **PLOTLY_TREEMAP_MARKER_BASE_COLORSCALE, - colors=git_commit_days_since_last_file_creation_per_directory["daysSinceLastCreation_limited"], + colors=plotly_values(git_commit_days_since_last_file_creation_per_directory["daysSinceLastCreation_limited"]), colorbar=dict(title="Days"), ), )) @@ -557,7 +565,7 @@ def generate_directory_commit_statistic_treemaps( create_treemap_commit_statistics_settings(git_commit_days_since_last_file_creation_per_directory), marker=dict( **PLOTLY_TREEMAP_MARKER_BASE_COLORSCALE, - colors=git_commit_days_since_last_file_creation_per_directory["daysSinceLastCreation_rank"], + colors=plotly_values(git_commit_days_since_last_file_creation_per_directory["daysSinceLastCreation_rank"]), colorbar=dict(title="Rank"), ), )) @@ -570,7 +578,7 @@ def generate_directory_commit_statistic_treemaps( create_treemap_commit_statistics_settings(git_commit_days_since_last_file_modification_per_directory), marker=dict( **PLOTLY_TREEMAP_MARKER_BASE_COLORSCALE, - colors=git_commit_days_since_last_file_modification_per_directory["daysSinceLastModification_limited"], + colors=plotly_values(git_commit_days_since_last_file_modification_per_directory["daysSinceLastModification_limited"]), colorbar=dict(title="Days"), ), )) @@ -583,7 +591,7 @@ def generate_directory_commit_statistic_treemaps( create_treemap_commit_statistics_settings(git_commit_days_since_last_file_modification_per_directory), marker=dict( **PLOTLY_TREEMAP_MARKER_BASE_COLORSCALE, - colors=git_commit_days_since_last_file_modification_per_directory["daysSinceLastModification_rank"], + colors=plotly_values(git_commit_days_since_last_file_modification_per_directory["daysSinceLastModification_rank"]), colorbar=dict(title="Rank"), ), )) @@ -633,7 +641,7 @@ def generate_cochange_treemaps( create_treemap_commit_statistics_settings(data_to_display), marker=dict( **PLOTLY_TREEMAP_MARKER_BASE_COLORSCALE, - colors=data_to_display["pairwiseChangeCommitCount_limited"], + colors=plotly_values(data_to_display["pairwiseChangeCommitCount_limited"]), colorbar=dict(title="Co-Changes"), ), )) @@ -646,7 +654,7 @@ def generate_cochange_treemaps( create_treemap_commit_statistics_settings(data_to_display), marker=dict( **PLOTLY_TREEMAP_MARKER_BASE_COLORSCALE, - colors=data_to_display["pairwiseChangeMaxLift_limited"], + colors=plotly_values(data_to_display["pairwiseChangeMaxLift_limited"]), colorbar=dict(title="Co-Change Lift"), ), )) @@ -662,7 +670,7 @@ def generate_cochange_treemaps( create_treemap_commit_statistics_settings(data_to_display), marker=dict( **PLOTLY_TREEMAP_MARKER_BASE_COLORSCALE, - colors=data_to_display["pairwiseChangeAverageLift_limited"], + colors=plotly_values(data_to_display["pairwiseChangeAverageLift_limited"]), colorbar=dict(title="Co-Change Lift"), ), )) @@ -685,8 +693,8 @@ def generate_files_per_commit_bar_chart( print(f"{SCRIPT_NAME}: Skipping files-per-commit bar chart — no data") return figure = plotly_graph_objects.Figure(plotly_graph_objects.Bar( - x=git_file_count_per_commit["filesPerCommit"].head(30), - y=git_file_count_per_commit["commitCount"].head(30), + x=plotly_values(git_file_count_per_commit["filesPerCommit"].head(30)), + y=plotly_values(git_file_count_per_commit["commitCount"].head(30)), )) figure.update_layout( **PLOTLY_MAIN_LAYOUT_BASE_SETTINGS, diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 000000000..eebd27ba6 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,32 @@ +[project] +name = "code-graph-analysis-pipeline" +version = "0.1.0" +requires-python = ">=3.12,<3.14" +dependencies = [ + # --- Jupyter (for notebook environments) --- + "ipykernel==7.2.0", + "matplotlib==3.10.8", + "numpy==2.2.5", + "pandas==2.3.3", + "pip==26.0.1", + "setuptools==80.10.2", # opentsne uses sklearn.base uses joblib uses distutils missing in Python >= 12 (TODO use native openTSNE?) + # --- Visualization --- + "wordcloud==1.9.6", + "monotonic==1.6", + "plotly[kaleido]==6.5.2", + "seaborn==0.13.2", # To visualize clustering results + # --- Machine Learning / Optimization --- + "scikit-learn==1.8.0", + "optuna==4.7.0", + "umap-learn==0.5.11", # Dimensionality reduction to visualize node embeddings in 2D + # --- Database connector --- + "neo4j==6.1.0", + # --- Native/scientific packages (may require compilation) --- + # These are included but may cause install errors in pip/venv + "shap==0.50.0", # For e.g. explaining anomaly detection results +] + +[tool.uv] +# uv is the primary Python package manager for this project. +# conda-environment.yml remains supported as an optional path. +# Run `uv sync --frozen` to install, `uv lock --check` to verify lockfile. diff --git a/renovate.json b/renovate.json index ba0a808af..dfe9d64ac 100644 --- a/renovate.json +++ b/renovate.json @@ -54,7 +54,7 @@ }, { "description": "Only use stable versions for Python", - "matchManagers": ["pip_requirements", "pip_setup", "poetry", "pipenv"], + "matchManagers": ["uv", "pip_setup", "poetry", "pipenv"], "ignoreUnstable": true } ], @@ -200,9 +200,9 @@ "datasourceTemplate": "maven" }, { - "description": "DISABLED Update conda environment for Python with pip version", + "description": "Update conda packages in conda-environment.yml (conda packages only, pip block excluded)", "customType": "regex", - "fileMatch": ["(^|/)conda-environment-temporarily-disabled\\.yml$"], + "fileMatch": ["(^|/)conda-environment\\.yml$"], "matchStrings": [ "\\s+-\\s+(?[\\w-]+)=(?[^\\s#=]+)[\\s#]+" ], @@ -212,6 +212,7 @@ }, { "description": "DISABLED Update pip nested packages inside conda-environment.yml.", + "customType": "regex", "fileMatch": ["(^|/)conda-environment-temporarily-disabled\\.yml$"], "matchStrings": [ "\\s+-\\s+(?[\\w-]+)==(?[^\\s#=]+)[\\s#]+" diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 5b78aae93..000000000 --- a/requirements.txt +++ /dev/null @@ -1,29 +0,0 @@ -# --- Core Python version --- -# NOTE: Python version must be >= 3.12 for compatibility -# This should be enforced by the user/environment, not pip -# NOTE: Keep this file in sync with conda-environment.yml - -# --- Core tools --- -matplotlib==3.10.8 -numpy==2.2.5 -pandas==2.3.3 -pip==26.0.1 -setuptools==80.10.2 # opentsne uses sklearn.base uses joblib uses distutils missing in Python >= 12 (TODO use native openTSNE?) - -# --- Visualization --- -wordcloud==1.9.6 -monotonic==1.6 -plotly[kaleido]==6.5.2 -seaborn==0.13.2 # To visualize clustering results - -# --- Machine Learning / Optimization --- -scikit-learn==1.8.0 -optuna==4.7.0 -umap-learn==0.5.11 # Dimensionality reduction to visualize node embeddings in 2D - -# --- Database connector --- -neo4j==6.1.0 - -# --- Native/scientific packages (may require compilation) --- -# These are included but may cause install errors in pip/venv -shap==0.50.0 # For e.g. explaining anomaly detection results \ No newline at end of file diff --git a/scripts/activateCondaEnvironment.sh b/scripts/activateCondaEnvironment.sh index e4e451477..529c56c1e 100755 --- a/scripts/activateCondaEnvironment.sh +++ b/scripts/activateCondaEnvironment.sh @@ -20,8 +20,11 @@ if [ "${PREPARE_CONDA_ENVIRONMENT}" = "false" ]; then return 0 fi -if [ "${USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV}" = "true" ]; then - echo "activateCondaEnvironment: Skipping activation. venv will be used instead of conda (USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV=true)." +PYTHON_PACKAGE_MANAGER=${PYTHON_PACKAGE_MANAGER:-"uv"} # Python package manager to use. Options: "uv" (default), "conda". Use "conda" to activate the Conda environment. +# DEPRECATED: USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV — use PYTHON_PACKAGE_MANAGER instead. + +if [ "${PYTHON_PACKAGE_MANAGER}" != "conda" ]; then + echo "activateCondaEnvironment: Skipping activation. PYTHON_PACKAGE_MANAGER=${PYTHON_PACKAGE_MANAGER} (expected 'conda')." # "return" needs to be used here instead of "exit". # This script is included in another script by using "source". # "exit" would end the main script, "return" just ends this sub script. diff --git a/scripts/activatePythonEnvironment.sh b/scripts/activatePythonEnvironment.sh deleted file mode 100755 index 50f27d988..000000000 --- a/scripts/activatePythonEnvironment.sh +++ /dev/null @@ -1,96 +0,0 @@ -#!/usr/bin/env bash - -# Activates the .venv environment (Python build-in virtual environments) with all packages necessary to run the included Python scripts. - -# Note: If the environment hadn't been created yet, it will use "requirements.txt" from the root directory to create the environment. - -# Requires operatingSystemFunctions.sh - -# Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands) -set -o errexit -o pipefail - -USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV=${USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV:-"false"} # Use "venv" for virtual Python environments ("true") or use an already prepared (e.g. conda) environment (default, "false"). - -if [ "${USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV}" = "false" ]; then - echo "activatePythonEnvironment: Skipping activation. An already activated environment and installed dependencies are expected e.g. by using conda (USE_VIRTUAL_PYTHON_ENVIRONMENT_VENV=false)." - # "return" needs to be used here instead of "exit". - # This script is included in another script by using "source". - # "exit" would end the main script, "return" just ends this sub script. - return 0 -fi - -## Get this "scripts" directory if not already set -# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. -# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes. -# This way non-standard tools like readlink aren't needed. -SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts -echo "activatePythonEnvironment: SCRIPTS_DIR=${SCRIPTS_DIR}" - -# Get the root directory by taking the path of this script and going one directory up. -ROOT_DIRECTORY=${ROOT_DIRECTORY:-"$(dirname "${SCRIPTS_DIR}")"} # Repository root directory -echo "activatePythonEnvironment: ROOT_DIRECTORY=${ROOT_DIRECTORY}" - -# Get the file name of the environment description file for the conda package and environment manager -# that contains all dependencies and their versions. -PYTHON_ENVIRONMENT_FILE=${PYTHON_ENVIRONMENT_FILE:-"${ROOT_DIRECTORY}/requirements.txt"} # Pip (package manager for Python) environment file path -if [ ! -f "${PYTHON_ENVIRONMENT_FILE}" ] ; then - echo "activatePythonEnvironment: Couldn't find environment file ${PYTHON_ENVIRONMENT_FILE}." - exit_failed -fi - -deactivate_conda_if_necessary() { - # Include operation system function to for example detect Windows. - source "${SCRIPTS_DIR}/operatingSystemFunctions.sh" - - # Determine the path to "conda" - if [ -n "${CONDA}" ]; then - if isWindows; then - pathToConda="${CONDA}\\Scripts\\" # the trailing backslash character is required - else - pathToConda="${CONDA}/bin/" # the trailing slash character is required - fi - else - pathToConda="" - fi - echo "activatePythonEnvironment: pathToConda=${pathToConda} (for deactivation)" - - scriptExtension=$(ifWindows ".bat" "") - echo "activatePythonEnvironment: scriptExtension=${scriptExtension}" - - if "${pathToConda}conda" deactivate >/dev/null 2>&1; then - # Call "deactivate" a second time to also deactivate the "base" environment - "${pathToConda}conda" deactivate >/dev/null 2>&1; - echo "activatePythonEnvironment: Conda deactivated" - else - echo "activatePythonEnvironment: Conda not found. Deactivation skipped" - fi -} - -VENV_DIRECTORY=".venv" - -# Create the virtual environment if needed -if [ ! -d "${ROOT_DIRECTORY}/${VENV_DIRECTORY}" ]; then - deactivate_conda_if_necessary - echo "activatePythonEnvironment: Creating ${VENV_DIRECTORY} environment..." - python -m venv "${ROOT_DIRECTORY}/${VENV_DIRECTORY}" -else - echo "activatePythonEnvironment: Already created ${VENV_DIRECTORY} environment." -fi - -# Activate the virtual environment if needed -if [ "${VIRTUAL_ENV}" != "${ROOT_DIRECTORY}/${VENV_DIRECTORY}" ]; then - echo "activatePythonEnvironment: Activate ${VENV_DIRECTORY} environment..." - source "${ROOT_DIRECTORY}/${VENV_DIRECTORY}/bin/activate" -else - echo "activatePythonEnvironment: Already activated ${VENV_DIRECTORY} environment." -fi - -# Install the virtual environment if needed -if pip install --dry-run --no-deps --requirement "${PYTHON_ENVIRONMENT_FILE}" 2>/dev/null | grep -q "Would install"; then - echo "activatePythonEnvironment: Install environment dependencies..." - pip install -q --requirement "${PYTHON_ENVIRONMENT_FILE}" -else - echo "activatePythonEnvironment: Already installed environment dependencies." -fi - -echo "activatePythonEnvironment: Python installation: $(which python)" \ No newline at end of file diff --git a/scripts/activateUvEnvironment.sh b/scripts/activateUvEnvironment.sh new file mode 100644 index 000000000..daee69eef --- /dev/null +++ b/scripts/activateUvEnvironment.sh @@ -0,0 +1,62 @@ +#!/usr/bin/env bash + +# Activates the uv-managed .venv environment with all packages from pyproject.toml necessary to run the included Python scripts. + +# Note: Requires operatingSystemFunctions.sh + +# Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands) +set -o errexit -o pipefail -o nounset +IFS=$'\n\t' + +PYTHON_PACKAGE_MANAGER=${PYTHON_PACKAGE_MANAGER:-"uv"} # Python package manager to use. Options: "uv" (default), "conda". Use "conda" to switch to the Conda-based activation. + +if [[ "${PYTHON_PACKAGE_MANAGER}" != "uv" ]]; then + echo "activateUvEnvironment: Skipping. PYTHON_PACKAGE_MANAGER=${PYTHON_PACKAGE_MANAGER} (expected 'uv')." + # "return" needs to be used here instead of "exit". + # This script is included in another script by using "source". + # "exit" would end the main script, "return" just ends this sub script. + return 0 +fi + +## Get this "scripts" directory if not already set +# Even if $BASH_SOURCE is made for Bourne-like shells it is also supported by others and therefore here the preferred solution. +# CDPATH reduces the scope of the cd command to potentially prevent unintended directory changes. +# This way non-standard tools like readlink aren't needed. +SCRIPTS_DIR=${SCRIPTS_DIR:-$( CDPATH=. cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd -P )} # Repository directory containing the shell scripts +echo "activateUvEnvironment: SCRIPTS_DIR=${SCRIPTS_DIR}" + +# Get the root directory by taking the path of this script and going one directory up. +ROOT_DIRECTORY=${ROOT_DIRECTORY:-"$(dirname "${SCRIPTS_DIR}")"} # Repository root directory +echo "activateUvEnvironment: ROOT_DIRECTORY=${ROOT_DIRECTORY}" + +# Check that uv is available. Hard-fail with install instructions if not. +if ! command -v uv &> /dev/null; then + echo "activateUvEnvironment: ERROR - 'uv' not found. Install from https://docs.astral.sh/uv/getting-started/installation/" + exit 1 +fi +echo "activateUvEnvironment: uv version=$(uv --version)" + +# Install/sync packages from pyproject.toml using the lockfile (frozen = no implicit updates). +echo "activateUvEnvironment: Running uv sync --frozen in ${ROOT_DIRECTORY}" +uv sync --frozen --project "${ROOT_DIRECTORY}" + +# Include operating system functions to detect Windows / Git Bash. +source "${SCRIPTS_DIR}/operatingSystemFunctions.sh" + +# Activate the .venv created by uv. +# On Windows (Git Bash/WSL) the activate script lives under Scripts/, on Unix under bin/. +if isWindows; then + venvActivate="${ROOT_DIRECTORY}/.venv/Scripts/activate" +else + venvActivate="${ROOT_DIRECTORY}/.venv/bin/activate" +fi + +if [ ! -f "${venvActivate}" ]; then + echo "activateUvEnvironment: ERROR - venv activate script not found at ${venvActivate}" + exit 1 +fi + +echo "activateUvEnvironment: Activating venv from ${venvActivate}" +# shellcheck disable=SC1090 +source "${venvActivate}" +echo "activateUvEnvironment: Python=$(python --version 2>&1)" diff --git a/scripts/checkCompatibility.sh b/scripts/checkCompatibility.sh index 835bd4034..73fbca2ca 100755 --- a/scripts/checkCompatibility.sh +++ b/scripts/checkCompatibility.sh @@ -141,18 +141,16 @@ checkRequiredCommand "npx" "Tool to run npm packages without installing them glo checkRequiredCommand "npm" "Node.js package manager (https://docs.npmjs.com/) for managing JavaScript packages" # Check dependencies for Python environments -icon=$(oneOf "conda" "venv") +icon=$(oneOf "uv" "conda") echo "" echo "${icon} Python environment dependencies (for ./analyze.sh --report Python):" +checkOptionalCommand "uv" "Python package manager (https://docs.astral.sh/uv/) for managing Python packages and environments" checkOptionalCommand "conda" "Conda package and environment manager (https://docs.conda.io/en/latest/)" -checkOptionalCommand "virtualenv" "Python virtual environment module (https://docs.python.org/3/library/venv.html)" # Check dependencies for Python reports -icon=$(allOf "python" "pip") echo "" -echo "${icon} Python reports dependencies (for ./analyze.sh --report Python):" -checkRequiredCommand "python" "Python interpreter (https://www.python.org/) for running Python scripts" -checkRequiredCommand "pip" "Python package installer (https://pip.pypa.io/en/stable/) for installing Python packages" +echo "ℹ️ Python reports dependencies (for ./analyze.sh --report Python):" +echo " Python and pip are managed by uv or conda — no separate installation needed." checkOptionalCommand "jupyter" "Jupyter Notebook (https://jupyter.org/) for manual interactive data analysis and visualization (will be available when the Python environment is activated)" # Check dependencies for visualization reports diff --git a/scripts/reports/compilations/PythonReports.sh b/scripts/reports/compilations/PythonReports.sh index 216de9e24..39ee0c692 100755 --- a/scripts/reports/compilations/PythonReports.sh +++ b/scripts/reports/compilations/PythonReports.sh @@ -1,9 +1,15 @@ #!/usr/bin/env bash # Runs all Python report scripts (no Chromium required). -# It only considers scripts in the "reports" and "domains" directories and their sub directories (overridable with REPORTS_SCRIPT_DIR and DOMAINS_DIRECTORY). - -# Requires activateCondaEnvironment.sh, activatePythonEnvironment.sh, reports/*.sh +# Discovers and executes Python report scripts matching *Python.sh or *Python.py patterns +# from the "reports" directory (REPORTS_SCRIPT_DIR) and all "domains" subdirectories (DOMAINS_DIRECTORY), +# recursively throughout their directory trees. +# When ANALYSIS_DOMAIN is set, runs only reports from that specific domain. +# Skips domains listed in ANALYSIS_DOMAINS_TO_SKIP. +# +# Requires: activateCondaEnvironment.sh, activateUvEnvironment.sh, and Python scripts matching: +# ${REPORTS_SCRIPT_DIR}/**/*Python.sh or ${REPORTS_SCRIPT_DIR}/**/*Python.py +# ${DOMAINS_DIRECTORY}/**/*Python.sh or ${DOMAINS_DIRECTORY}/**/*Python.py # Fail on any error ("-e" = exit on first error, "-o pipefail" exist on errors within piped commands) set -o errexit -o pipefail @@ -34,12 +40,12 @@ echo "${SCRIPT_NAME}: DOMAINS_DIRECTORY=${DOMAINS_DIRECTORY}" echo "${SCRIPT_NAME}: ANALYSIS_DOMAIN=${ANALYSIS_DOMAIN}" echo "${SCRIPT_NAME}: ANALYSIS_DOMAINS_TO_SKIP=${ANALYSIS_DOMAINS_TO_SKIP:-}" -# Create and activate (if necessary) a virtual environment (Conda or venv). +# Create and activate (if necessary) a virtual environment (Conda or uv). # For Conda, the environment name is taken from the environment variable CODEGRAPH_CONDA_ENVIRONMENT (default "codegraph") # and the dependencies are listed in the root directory file "conda-environment.yml". -# For venv, the dependencies are listed in the root directory file "requirements.txt". +# For uv (default), the dependencies are listed in the root directory file "pyproject.toml". time source 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