From dff7bde6cf667ec098fbd49d4637d7f78371225b Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Mon, 25 Nov 2024 23:41:07 +0000 Subject: [PATCH 01/15] WIP: See if we can use uv lockfile --- .github/actions/install-aiida-core/action.yml | 28 +- .github/workflows/ci-code.yml | 5 +- uv.lock | 4841 +++++++++++++++++ 3 files changed, 4854 insertions(+), 20 deletions(-) create mode 100644 uv.lock diff --git a/.github/actions/install-aiida-core/action.yml b/.github/actions/install-aiida-core/action.yml index 3c82771cdc..40a7e3b5b9 100644 --- a/.github/actions/install-aiida-core/action.yml +++ b/.github/actions/install-aiida-core/action.yml @@ -12,8 +12,9 @@ inputs: required: false # NOTE: Hard-learned lesson: we cannot use type=boolean here, apparently :-( # https://stackoverflow.com/a/76294014 + # TODO: Rename this to 'from-lock' from-requirements: - description: Install aiida-core dependencies from pre-compiled requirements.txt file + description: Install aiida-core dependencies from a uv lock file default: 'true' required: false @@ -25,26 +26,17 @@ runs: with: python-version: ${{ inputs.python-version }} - - name: Install uv installer - run: curl --proto '=https' --tlsv1.2 -LsSf https://${{ env.UV_URL }} | sh - env: - UV_VERSION: 0.2.9 - UV_URL: github.com/astral-sh/uv/releases/download/$UV_VERSION/uv-installer.sh - shell: bash + - name: Set up uv + uses: astral-sh/setup-uv@v3 + with: + version: 0.5.4 - - name: Install dependencies from requirements-py-*.txt + - name: Install dependencies from uv lock if: ${{ inputs.from-requirements == 'true' }} - run: uv pip install --system -r requirements/requirements-py-${{ inputs.python-version }}.txt + run: uv sync --locked shell: bash - name: Install aiida-core - run: uv pip install --system ${{ env.NO_DEPS }} -e .${{ inputs.extras }} - env: - # Don't install dependencies if they were installed through requirements file AND - # if no extras are required. - # - # If this syntax looks weird to you, dear reader, know that this is - # GHA's way to do ternary operator. :-/ - # https://docs.github.com/en/actions/learn-github-actions/expressions#example - NO_DEPS: ${{ (inputs.from-requirements == 'true' && inputs.extras == '') && '--no-deps' || '' }} + if: ${{ inputs.from-requirements != 'true' }} + run: uv pip install --system -e .${{ inputs.extras }} shell: bash diff --git a/.github/workflows/ci-code.yml b/.github/workflows/ci-code.yml index a8d0cb9a08..e61ca6d2e6 100644 --- a/.github/workflows/ci-code.yml +++ b/.github/workflows/ci-code.yml @@ -34,6 +34,7 @@ jobs: - name: Install utils/ dependencies run: pip install -r utils/requirements.txt + # TODO: Change this to make sure that the lock is up-to-date - name: Check requirements files id: check_reqs run: python ./utils/dependency_management.py check-requirements DEFAULT @@ -104,7 +105,7 @@ jobs: AIIDA_WARN_v3: 1 # Python 3.12 has a performance regression when running with code coverage # so run code coverage only for python 3.9. - run: pytest --db-backend psql 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hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931", size = 9630 }, +] From 368dff3a7c9dd59db9a1184daf31961a9c89c7b6 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Tue, 26 Nov 2024 14:34:15 +0000 Subject: [PATCH 02/15] Add pre-commit extra --- .github/actions/install-aiida-core/action.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/actions/install-aiida-core/action.yml b/.github/actions/install-aiida-core/action.yml index 40a7e3b5b9..189d22ca2f 100644 --- a/.github/actions/install-aiida-core/action.yml +++ b/.github/actions/install-aiida-core/action.yml @@ -33,7 +33,7 @@ runs: - name: Install dependencies from uv lock if: ${{ inputs.from-requirements == 'true' }} - run: uv sync --locked + run: uv sync --locked --extra pre-commit shell: bash - name: Install aiida-core From 63f9929dd8485a2132930e50930d0bdb5fea8b2d Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Tue, 26 Nov 2024 16:40:18 +0000 Subject: [PATCH 03/15] Activate the environment --- .github/workflows/ci-code.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-code.yml b/.github/workflows/ci-code.yml index e61ca6d2e6..c778c0b3ca 100644 --- a/.github/workflows/ci-code.yml +++ b/.github/workflows/ci-code.yml @@ -97,7 +97,7 @@ jobs: python-version: ${{ matrix.python-version }} - name: Setup environment - run: .github/workflows/setup.sh + run: source .venv/bin/activate && .github/workflows/setup.sh - name: Run test suite env: From 924f1bb005d4f9ce09fbe9999ebe2b398112cf5a Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Tue, 26 Nov 2024 16:42:30 +0000 Subject: [PATCH 04/15] s/from-requirements/from-lock/ --- .github/actions/install-aiida-core/action.yml | 7 +++---- .github/workflows/ci-code.yml | 2 +- .github/workflows/docs-build.yml | 2 +- .github/workflows/release.yml | 2 +- .github/workflows/test-install.yml | 2 +- 5 files changed, 7 insertions(+), 8 deletions(-) diff --git a/.github/actions/install-aiida-core/action.yml b/.github/actions/install-aiida-core/action.yml index 189d22ca2f..aae701b540 100644 --- a/.github/actions/install-aiida-core/action.yml +++ b/.github/actions/install-aiida-core/action.yml @@ -12,8 +12,7 @@ inputs: required: false # NOTE: Hard-learned lesson: we cannot use type=boolean here, apparently :-( # https://stackoverflow.com/a/76294014 - # TODO: Rename this to 'from-lock' - from-requirements: + from-lock: description: Install aiida-core dependencies from a uv lock file default: 'true' required: false @@ -32,11 +31,11 @@ runs: version: 0.5.4 - name: Install dependencies from uv lock - if: ${{ inputs.from-requirements == 'true' }} + if: ${{ inputs.from-lock == 'true' }} run: uv sync --locked --extra pre-commit shell: bash - name: Install aiida-core - if: ${{ inputs.from-requirements != 'true' }} + if: ${{ inputs.from-lock != 'true' }} run: uv pip install --system -e .${{ inputs.extras }} shell: bash diff --git a/.github/workflows/ci-code.yml b/.github/workflows/ci-code.yml index c778c0b3ca..8ae362e0c7 100644 --- a/.github/workflows/ci-code.yml +++ b/.github/workflows/ci-code.yml @@ -156,7 +156,7 @@ jobs: uses: ./.github/actions/install-aiida-core with: python-version: '3.12' - from-requirements: 'false' + from-lock: 'false' - name: Run verdi tests run: | diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml index bf1cce6d4c..a3b2b5e7aa 100644 --- a/.github/workflows/docs-build.yml +++ b/.github/workflows/docs-build.yml @@ -25,7 +25,7 @@ jobs: with: python-version: '3.9' extras: '[docs,tests,rest,atomic_tools]' - from-requirements: 'false' + from-lock: 'false' - name: Build HTML docs id: linkcheck diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index c47595baee..d4951d1614 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -42,7 +42,7 @@ jobs: with: python-version: '3.11' extras: '[pre-commit]' - from-requirements: 'false' + from-lock: 'false' - name: Run pre-commit run: pre-commit run --all-files || ( git status --short ; git diff ; exit 1 ) diff --git a/.github/workflows/test-install.yml b/.github/workflows/test-install.yml index d315a50691..7b8bc447b8 100644 --- a/.github/workflows/test-install.yml +++ b/.github/workflows/test-install.yml @@ -220,7 +220,7 @@ jobs: with: python-version: ${{ matrix.python-version }} extras: '[atomic_tools,docs,notebook,rest,tests,tui]' - from-requirements: 'false' + from-lock: 'false' - name: Setup AiiDA environment run: .github/workflows/setup.sh From 47095d697c540ecc411c2ee27c3d23c001b1fb9e Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Thu, 28 Nov 2024 18:51:58 +0000 Subject: [PATCH 05/15] git rm -r requirements/ --- requirements/README.md | 7 - requirements/requirements-py-3.10.txt | 215 ------------------------- requirements/requirements-py-3.11.txt | 213 ------------------------- requirements/requirements-py-3.12.txt | 213 ------------------------- requirements/requirements-py-3.9.txt | 217 -------------------------- 5 files changed, 865 deletions(-) delete mode 100644 requirements/README.md delete mode 100644 requirements/requirements-py-3.10.txt delete mode 100644 requirements/requirements-py-3.11.txt delete mode 100644 requirements/requirements-py-3.12.txt delete mode 100644 requirements/requirements-py-3.9.txt diff --git a/requirements/README.md b/requirements/README.md deleted file mode 100644 index 678ba5aa1a..0000000000 --- a/requirements/README.md +++ /dev/null @@ -1,7 +0,0 @@ -# README - -The `requirements-*.txt` files within this directory define the Python environment used for the *continuous integration tests* of this package. Note: For instructions on how to install the package for regular use, please see the documentation. - -The consistency of the requirements defined here with the dependencies defined in the `pyproject.toml` file is checked automatically as part of the continuous integration workflow. - -https://github.com/aiidateam/aiida-core/wiki/AiiDA-Dependency-Management diff --git a/requirements/requirements-py-3.10.txt b/requirements/requirements-py-3.10.txt deleted file mode 100644 index b2408e8087..0000000000 --- a/requirements/requirements-py-3.10.txt +++ /dev/null @@ -1,215 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.10 -# by the following command: -# -# pip-compile --extra=atomic_tools --extra=docs --extra=notebook --extra=rest --extra=tests --no-annotate --output-file=requirements/requirements-py-3.10.txt pyproject.toml -# -accessible-pygments==0.0.5 -aiida-export-migration-tests==0.9.0 -aio-pika==9.4.0 -aiormq==6.8.0 -alabaster==0.7.13 -alembic==1.11.1 -aniso8601==9.0.1 -annotated-types==0.7.0 -anyio==3.7.0 -archive-path==0.4.2 -argon2-cffi==21.3.0 -argon2-cffi-bindings==21.2.0 -ase==3.22.1 -asn1crypto==1.5.1 -asttokens==2.2.1 -async-generator==1.10 -attrs==23.1.0 -babel==2.12.1 -backcall==0.2.0 -bcrypt==4.0.1 -beautifulsoup4==4.12.2 -bleach==6.0.0 -blinker==1.6.2 -certifi==2023.5.7 -cffi==1.15.1 -charset-normalizer==3.1.0 -circus==0.18.0 -click==8.1.3 -click-spinner==0.1.10 -comm==0.1.3 -contourpy==1.1.0 -coverage[toml]==7.4.1 -cryptography==41.0.1 -cycler==0.11.0 -debugpy==1.6.7 -decorator==5.1.1 -defusedxml==0.7.1 -deprecation==2.1.0 -disk-objectstore==1.2.0 -docstring-parser==0.15 -docutils==0.20.1 -exceptiongroup==1.1.1 -executing==1.2.0 -fastjsonschema==2.17.1 -flask==2.3.2 -flask-cors==3.0.10 -flask-restful==0.3.10 -fonttools==4.40.0 -future==0.18.3 -graphviz==0.20.1 -greenlet==2.0.2 -idna==3.4 -imagesize==1.4.1 -importlib-metadata==6.8.0 -iniconfig==2.0.0 -ipykernel==6.23.2 -ipython==8.14.0 -ipython-genutils==0.2.0 -ipywidgets==8.0.6 -itsdangerous==2.1.2 -jedi==0.18.2 -jinja2==3.1.2 -joblib==1.4.2 -jsonschema[format-nongpl]==3.2.0 -jupyter==1.0.0 -jupyter-cache==0.6.1 -jupyter-client==8.2.0 -jupyter-console==6.6.3 -jupyter-core==5.3.1 -jupyter-events==0.6.3 -jupyter-server==2.6.0 -jupyter-server-terminals==0.4.4 -jupyterlab-pygments==0.2.2 -jupyterlab-widgets==3.0.7 -kiwipy[rmq]==0.8.4 -kiwisolver==1.4.4 -latexcodec==2.0.1 -mako==1.2.4 -markdown-it-py==3.0.0 -markupsafe==2.1.3 -matplotlib==3.7.1 -matplotlib-inline==0.1.6 -mdit-py-plugins==0.4.0 -mdurl==0.1.2 -mistune==3.0.1 -monty==2023.9.25 -mpmath==1.3.0 -multidict==6.0.4 -myst-nb==1.0.0 -myst-parser==2.0.0 -nbclassic==1.0.0 -nbclient==0.7.4 -nbconvert==7.6.0 -nbformat==5.9.0 -nest-asyncio==1.5.6 -networkx==3.1 -notebook==6.5.4 -notebook-shim==0.2.3 -numpy==1.25.0 -overrides==7.3.1 -packaging==23.1 -palettable==3.3.3 -pamqp==3.3.0 -pandas==2.0.2 -pandocfilters==1.5.0 -paramiko==3.4.1 -parso==0.8.3 -pexpect==4.8.0 -pg8000==1.29.8 -pgsu==0.3.0 -pgtest==1.3.2 -pickleshare==0.7.5 -pillow==9.5.0 -platformdirs==3.6.0 -plotly==5.15.0 -pluggy==1.0.0 -plumpy==0.22.3 -prometheus-client==0.17.0 -prompt-toolkit==3.0.38 -psutil==5.9.5 -psycopg[binary]==3.1.18 -ptyprocess==0.7.0 -pure-eval==0.2.2 -py-cpuinfo==9.0.0 -pybtex==0.24.0 -pycifrw==4.4.5 -pycparser==2.21 -pydantic==2.4.0 -pydantic-core==2.10.0 -pydata-sphinx-theme==0.15.1 -pygments==2.15.1 -pymatgen==2023.9.25 -pympler==1.0.1 -pymysql==0.9.3 -pynacl==1.5.0 -pyparsing==3.1.1 -pyrsistent==0.19.3 -pytest==7.3.2 -pytest-asyncio==0.16.0 -pytest-benchmark==4.0.0 -pytest-cov==4.1.0 -pytest-datadir==1.4.1 -pytest-regressions==2.4.2 -pytest-rerunfailures==12.0 -pytest-timeout==2.2.0 -python-dateutil==2.8.2 -python-json-logger==2.0.7 -python-memcached==1.59 -pytray==0.3.4 -pytz==2021.3 -pyyaml==6.0 -pyzmq==25.1.0 -qtconsole==5.4.3 -qtpy==2.3.1 -requests==2.31.0 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -ruamel-yaml==0.17.32 -ruamel-yaml-clib==0.2.7 -scipy==1.10.1 -scramp==1.4.4 -seekpath==1.9.7 -send2trash==1.8.2 -shortuuid==1.0.11 -six==1.16.0 -sniffio==1.3.0 -snowballstemmer==2.2.0 -soupsieve==2.4.1 -spglib==2.0.2 -sphinx==7.2.6 -sphinx-copybutton==0.5.2 -sphinx-design==0.5.0 -sphinx-intl==2.1.0 -sphinx-notfound-page==1.0.0 -sphinx-sqlalchemy==0.2.0 -sphinxcontrib-applehelp==1.0.4 -sphinxcontrib-devhelp==1.0.2 -sphinxcontrib-htmlhelp==2.0.1 -sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==1.0.3 -sphinxcontrib-serializinghtml==1.1.9 -sphinxext-rediraffe==0.2.7 -sqlalchemy==2.0.23 -stack-data==0.6.2 -sympy==1.12 -tabulate==0.9.0 -tenacity==8.2.2 -terminado==0.17.1 -tinycss2==1.2.1 -tomli==2.0.1 -tornado==6.3.2 -tqdm==4.65.0 -traitlets==5.9.0 -typing-extensions==4.6.3 -tzdata==2023.3 -uncertainties==3.1.7 -upf-to-json==0.9.5 -urllib3==2.0.3 -wcwidth==0.2.6 -webencodings==0.5.1 -websocket-client==1.6.0 -werkzeug==2.3.6 -widgetsnbextension==4.0.7 -wrapt==1.15.0 -yarl==1.9.2 -zipp==3.15.0 - -# The following packages are considered to be unsafe in a requirements file: -# setuptools diff --git a/requirements/requirements-py-3.11.txt b/requirements/requirements-py-3.11.txt deleted file mode 100644 index 24acc25a6b..0000000000 --- a/requirements/requirements-py-3.11.txt +++ /dev/null @@ -1,213 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.11 -# by the following command: -# -# pip-compile --extra=atomic_tools --extra=docs --extra=notebook --extra=rest --extra=tests --no-annotate --output-file=requirements/requirements-py-3.9.txt pyproject.toml -# -accessible-pygments==0.0.5 -aiida-export-migration-tests==0.9.0 -aio-pika==9.4.0 -aiormq==6.8.0 -alabaster==0.7.13 -alembic==1.11.1 -aniso8601==9.0.1 -annotated-types==0.7.0 -anyio==3.7.0 -archive-path==0.4.2 -argon2-cffi==21.3.0 -argon2-cffi-bindings==21.2.0 -ase==3.22.1 -asn1crypto==1.5.1 -asttokens==2.2.1 -async-generator==1.10 -attrs==23.1.0 -babel==2.12.1 -backcall==0.2.0 -bcrypt==4.0.1 -beautifulsoup4==4.12.2 -bleach==6.0.0 -blinker==1.6.2 -certifi==2023.5.7 -cffi==1.15.1 -charset-normalizer==3.1.0 -circus==0.18.0 -click==8.1.3 -click-spinner==0.1.10 -comm==0.1.3 -contourpy==1.1.0 -coverage[toml]==7.4.1 -cryptography==41.0.1 -cycler==0.11.0 -debugpy==1.6.7 -decorator==5.1.1 -defusedxml==0.7.1 -deprecation==2.1.0 -disk-objectstore==1.2.0 -docstring-parser==0.15 -docutils==0.20.1 -executing==1.2.0 -fastjsonschema==2.17.1 -flask==2.3.2 -flask-cors==3.0.10 -flask-restful==0.3.10 -fonttools==4.40.0 -future==0.18.3 -graphviz==0.20.1 -greenlet==2.0.2 -idna==3.4 -imagesize==1.4.1 -importlib-metadata==6.8.0 -iniconfig==2.0.0 -ipykernel==6.23.2 -ipython==8.14.0 -ipython-genutils==0.2.0 -ipywidgets==8.0.6 -itsdangerous==2.1.2 -jedi==0.18.2 -jinja2==3.1.2 -joblib==1.4.2 -jsonschema[format-nongpl]==3.2.0 -jupyter==1.0.0 -jupyter-cache==0.6.1 -jupyter-client==8.2.0 -jupyter-console==6.6.3 -jupyter-core==5.3.1 -jupyter-events==0.6.3 -jupyter-server==2.6.0 -jupyter-server-terminals==0.4.4 -jupyterlab-pygments==0.2.2 -jupyterlab-widgets==3.0.7 -kiwipy[rmq]==0.8.4 -kiwisolver==1.4.4 -latexcodec==2.0.1 -mako==1.2.4 -markdown-it-py==3.0.0 -markupsafe==2.1.3 -matplotlib==3.7.1 -matplotlib-inline==0.1.6 -mdit-py-plugins==0.4.0 -mdurl==0.1.2 -mistune==3.0.1 -monty==2023.9.25 -mpmath==1.3.0 -multidict==6.0.4 -myst-nb==1.0.0 -myst-parser==2.0.0 -nbclassic==1.0.0 -nbclient==0.7.4 -nbconvert==7.6.0 -nbformat==5.9.0 -nest-asyncio==1.5.6 -networkx==3.1 -notebook==6.5.4 -notebook-shim==0.2.3 -numpy==1.25.0 -overrides==7.3.1 -packaging==23.1 -palettable==3.3.3 -pamqp==3.3.0 -pandas==2.0.2 -pandocfilters==1.5.0 -paramiko==3.4.1 -parso==0.8.3 -pexpect==4.8.0 -pg8000==1.29.8 -pgsu==0.3.0 -pgtest==1.3.2 -pickleshare==0.7.5 -pillow==9.5.0 -platformdirs==3.6.0 -plotly==5.15.0 -pluggy==1.0.0 -plumpy==0.22.3 -prometheus-client==0.17.0 -prompt-toolkit==3.0.38 -psutil==5.9.5 -psycopg[binary]==3.1.18 -ptyprocess==0.7.0 -pure-eval==0.2.2 -py-cpuinfo==9.0.0 -pybtex==0.24.0 -pycifrw==4.4.5 -pycparser==2.21 -pydantic==2.4.0 -pydantic-core==2.10.0 -pydata-sphinx-theme==0.15.1 -pygments==2.15.1 -pymatgen==2023.9.25 -pympler==1.0.1 -pymysql==0.9.3 -pynacl==1.5.0 -pyparsing==3.1.1 -pyrsistent==0.19.3 -pytest==7.3.2 -pytest-asyncio==0.16.0 -pytest-benchmark==4.0.0 -pytest-cov==4.1.0 -pytest-datadir==1.4.1 -pytest-regressions==2.4.2 -pytest-rerunfailures==12.0 -pytest-timeout==2.2.0 -python-dateutil==2.8.2 -python-json-logger==2.0.7 -python-memcached==1.59 -pytray==0.3.4 -pytz==2021.3 -pyyaml==6.0 -pyzmq==25.1.0 -qtconsole==5.4.3 -qtpy==2.3.1 -requests==2.31.0 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -ruamel-yaml==0.17.32 -ruamel-yaml-clib==0.2.7 -scipy==1.10.1 -scramp==1.4.4 -seekpath==1.9.7 -send2trash==1.8.2 -shortuuid==1.0.11 -six==1.16.0 -sniffio==1.3.0 -snowballstemmer==2.2.0 -soupsieve==2.4.1 -spglib==2.0.2 -sphinx==7.2.6 -sphinx-copybutton==0.5.2 -sphinx-design==0.5.0 -sphinx-intl==2.1.0 -sphinx-notfound-page==1.0.0 -sphinx-sqlalchemy==0.2.0 -sphinxcontrib-applehelp==1.0.4 -sphinxcontrib-devhelp==1.0.2 -sphinxcontrib-htmlhelp==2.0.1 -sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==1.0.3 -sphinxcontrib-serializinghtml==1.1.9 -sphinxext-rediraffe==0.2.7 -sqlalchemy==2.0.23 -stack-data==0.6.2 -sympy==1.12 -tabulate==0.9.0 -tenacity==8.2.2 -terminado==0.17.1 -tinycss2==1.2.1 -tornado==6.3.2 -tqdm==4.65.0 -traitlets==5.9.0 -typing-extensions==4.6.3 -tzdata==2023.3 -uncertainties==3.1.7 -upf-to-json==0.9.5 -urllib3==2.0.3 -wcwidth==0.2.6 -webencodings==0.5.1 -websocket-client==1.6.0 -werkzeug==2.3.6 -widgetsnbextension==4.0.7 -wrapt==1.15.0 -yarl==1.9.2 -zipp==3.15.0 - -# The following packages are considered to be unsafe in a requirements file: -# setuptools diff --git a/requirements/requirements-py-3.12.txt b/requirements/requirements-py-3.12.txt deleted file mode 100644 index 3f5d72ebb6..0000000000 --- a/requirements/requirements-py-3.12.txt +++ /dev/null @@ -1,213 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.12 -# by the following command: -# -# pip-compile --extra=atomic_tools --extra=docs --extra=notebook --extra=rest --extra=tests --no-annotate --output-file=requirements/requirements-py-3.12.txt pyproject.toml -# -accessible-pygments==0.0.4 -aiida-export-migration-tests==0.9.0 -aio-pika==9.4.0 -aiormq==6.8.0 -alabaster==0.7.13 -alembic==1.12.0 -aniso8601==9.0.1 -annotated-types==0.7.0 -anyio==4.0.0 -archive-path==0.4.2 -argon2-cffi==23.1.0 -argon2-cffi-bindings==21.2.0 -ase==3.22.1 -asn1crypto==1.5.1 -asttokens==2.4.0 -async-generator==1.10 -attrs==23.1.0 -babel==2.13.1 -backcall==0.2.0 -bcrypt==4.0.1 -beautifulsoup4==4.12.2 -bleach==6.1.0 -blinker==1.6.3 -certifi==2023.7.22 -cffi==1.16.0 -charset-normalizer==3.3.1 -circus==0.18.0 -click==8.1.7 -click-spinner==0.1.10 -comm==0.1.4 -contourpy==1.1.1 -coverage[toml]==7.4.1 -cryptography==41.0.5 -cycler==0.12.1 -debugpy==1.8.0 -decorator==5.1.1 -defusedxml==0.7.1 -deprecation==2.1.0 -disk-objectstore==1.2.0 -docstring-parser==0.15 -docutils==0.20.1 -executing==2.0.0 -fastjsonschema==2.18.1 -flask==2.3.3 -flask-cors==3.0.10 -flask-restful==0.3.10 -fonttools==4.43.1 -future==0.18.3 -graphviz==0.20.1 -greenlet==3.0.0 -idna==3.4 -imagesize==1.4.1 -importlib-metadata==6.8.0 -iniconfig==2.0.0 -ipykernel==6.25.2 -ipython==8.16.1 -ipython-genutils==0.2.0 -ipywidgets==8.1.1 -itsdangerous==2.1.2 -jedi==0.18.2 -jinja2==3.1.2 -joblib==1.3.2 -jsonschema[format-nongpl]==3.2.0 -jupyter==1.0.0 -jupyter-cache==0.6.1 -jupyter-client==8.4.0 -jupyter-console==6.6.3 -jupyter-core==5.4.0 -jupyter-events==0.6.3 -jupyter-server==2.8.0 -jupyter-server-terminals==0.4.4 -jupyterlab-pygments==0.2.2 -jupyterlab-widgets==3.0.9 -kiwipy[rmq]==0.8.4 -kiwisolver==1.4.5 -latexcodec==2.0.1 -mako==1.2.4 -markdown-it-py==3.0.0 -markupsafe==2.1.3 -matplotlib==3.8.0 -matplotlib-inline==0.1.6 -mdit-py-plugins==0.4.0 -mdurl==0.1.2 -mistune==3.0.2 -monty==2023.9.25 -mpmath==1.3.0 -multidict==6.0.4 -myst-nb==1.0.0 -myst-parser==2.0.0 -nbclassic==1.0.0 -nbclient==0.7.4 -nbconvert==7.9.2 -nbformat==5.9.2 -nest-asyncio==1.5.8 -networkx==3.2 -notebook==6.5.4 -notebook-shim==0.2.3 -numpy==1.26.1 -overrides==7.4.0 -packaging==23.2 -palettable==3.3.3 -pamqp==3.3.0 -pandas==2.1.1 -pandocfilters==1.5.0 -paramiko==3.4.1 -parso==0.8.3 -pexpect==4.8.0 -pg8000==1.30.2 -pgsu==0.3.0 -pgtest==1.3.2 -pickleshare==0.7.5 -pillow==10.1.0 -platformdirs==3.11.0 -plotly==5.17.0 -pluggy==1.3.0 -plumpy==0.22.3 -prometheus-client==0.17.1 -prompt-toolkit==3.0.39 -psutil==5.9.6 -psycopg[binary]==3.1.18 -ptyprocess==0.7.0 -pure-eval==0.2.2 -py-cpuinfo==9.0.0 -pybtex==0.24.0 -pycifrw==4.4.5 -pycparser==2.21 -pydantic==2.4.0 -pydantic-core==2.10.0 -pydata-sphinx-theme==0.15.1 -pygments==2.16.1 -pymatgen==2023.10.11 -pympler==1.0.1 -pymysql==0.9.3 -pynacl==1.5.0 -pyparsing==3.1.1 -pyrsistent==0.19.3 -pytest==7.4.2 -pytest-asyncio==0.16.0 -pytest-benchmark==4.0.0 -pytest-cov==4.1.0 -pytest-datadir==1.5.0 -pytest-regressions==2.5.0 -pytest-rerunfailures==12.0 -pytest-timeout==2.2.0 -python-dateutil==2.8.2 -python-json-logger==2.0.7 -python-memcached==1.59 -pytray==0.3.4 -pytz==2021.3 -pyyaml==6.0.1 -pyzmq==25.1.1 -qtconsole==5.4.4 -qtpy==2.4.1 -requests==2.31.0 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -ruamel-yaml==0.18.2 -ruamel-yaml-clib==0.2.8 -scipy==1.11.3 -scramp==1.4.4 -seekpath==1.9.7 -send2trash==1.8.2 -shortuuid==1.0.11 -six==1.16.0 -sniffio==1.3.0 -snowballstemmer==2.2.0 -soupsieve==2.5 -spglib==2.1.0 -sphinx==7.2.6 -sphinx-copybutton==0.5.2 -sphinx-design==0.5.0 -sphinx-intl==2.1.0 -sphinx-notfound-page==1.0.0 -sphinx-sqlalchemy==0.2.0 -sphinxcontrib-applehelp==1.0.4 -sphinxcontrib-devhelp==1.0.2 -sphinxcontrib-htmlhelp==2.0.1 -sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==1.0.3 -sphinxcontrib-serializinghtml==1.1.9 -sphinxext-rediraffe==0.2.7 -sqlalchemy==2.0.23 -stack-data==0.6.3 -sympy==1.12 -tabulate==0.9.0 -tenacity==8.2.3 -terminado==0.17.1 -tinycss2==1.2.1 -tornado==6.3.3 -tqdm==4.66.1 -traitlets==5.11.2 -typing-extensions==4.8.0 -tzdata==2023.3 -uncertainties==3.1.7 -upf-to-json==0.9.5 -urllib3==2.0.7 -wcwidth==0.2.8 -webencodings==0.5.1 -websocket-client==1.6.4 -werkzeug==3.0.0 -widgetsnbextension==4.0.9 -wrapt==1.15.0 -yarl==1.9.2 -zipp==3.17.0 - -# The following packages are considered to be unsafe in a requirements file: -# setuptools diff --git a/requirements/requirements-py-3.9.txt b/requirements/requirements-py-3.9.txt deleted file mode 100644 index 3087e62844..0000000000 --- a/requirements/requirements-py-3.9.txt +++ /dev/null @@ -1,217 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.9 -# by the following command: -# -# pip-compile --extra=atomic_tools --extra=docs --extra=notebook --extra=rest --extra=tests --no-annotate --output-file=requirements/requirements-py-3.9.txt pyproject.toml -# -accessible-pygments==0.0.5 -aiida-export-migration-tests==0.9.0 -aio-pika==9.4.0 -aiormq==6.8.0 -alabaster==0.7.13 -alembic==1.11.1 -aniso8601==9.0.1 -annotated-types==0.7.0 -anyio==3.7.0 -archive-path==0.4.2 -argon2-cffi==21.3.0 -argon2-cffi-bindings==21.2.0 -ase==3.22.1 -asn1crypto==1.5.1 -asttokens==2.2.1 -async-generator==1.10 -attrs==23.1.0 -babel==2.12.1 -backcall==0.2.0 -bcrypt==4.0.1 -beautifulsoup4==4.12.2 -bleach==6.0.0 -blinker==1.6.2 -certifi==2023.5.7 -cffi==1.15.1 -charset-normalizer==3.1.0 -circus==0.18.0 -click==8.1.3 -click-spinner==0.1.10 -comm==0.1.3 -contourpy==1.1.0 -coverage[toml]==7.4.1 -cryptography==41.0.1 -cycler==0.11.0 -debugpy==1.6.7 -decorator==5.1.1 -defusedxml==0.7.1 -deprecation==2.1.0 -disk-objectstore==1.2.0 -docstring-parser==0.15 -docutils==0.20.1 -exceptiongroup==1.2.1 -executing==1.2.0 -fastjsonschema==2.17.1 -flask==2.3.2 -flask-cors==3.0.10 -flask-restful==0.3.10 -fonttools==4.40.0 -future==0.18.3 -get-annotations==0.1.2 ; python_version < "3.10" -graphviz==0.20.1 -greenlet==2.0.2 -idna==3.4 -imagesize==1.4.1 -importlib-metadata==6.8.0 -importlib-resources==6.4.0 -iniconfig==2.0.0 -ipykernel==6.23.2 -ipython==8.14.0 -ipython-genutils==0.2.0 -ipywidgets==8.0.6 -itsdangerous==2.1.2 -jedi==0.18.2 -jinja2==3.1.2 -joblib==1.4.2 -jsonschema[format-nongpl]==3.2.0 -jupyter==1.0.0 -jupyter-cache==0.6.1 -jupyter-client==8.2.0 -jupyter-console==6.6.3 -jupyter-core==5.3.1 -jupyter-events==0.6.3 -jupyter-server==2.6.0 -jupyter-server-terminals==0.4.4 -jupyterlab-pygments==0.2.2 -jupyterlab-widgets==3.0.7 -kiwipy[rmq]==0.8.4 -kiwisolver==1.4.4 -latexcodec==2.0.1 -mako==1.2.4 -markdown-it-py==3.0.0 -markupsafe==2.1.3 -matplotlib==3.7.1 -matplotlib-inline==0.1.6 -mdit-py-plugins==0.4.0 -mdurl==0.1.2 -mistune==3.0.1 -monty==2023.9.25 -mpmath==1.3.0 -multidict==6.0.4 -myst-nb==1.0.0 -myst-parser==2.0.0 -nbclassic==1.0.0 -nbclient==0.7.4 -nbconvert==7.6.0 -nbformat==5.9.0 -nest-asyncio==1.5.6 -networkx==3.1 -notebook==6.5.4 -notebook-shim==0.2.3 -numpy==1.25.0 -overrides==7.3.1 -packaging==23.1 -palettable==3.3.3 -pamqp==3.3.0 -pandas==2.0.2 -pandocfilters==1.5.0 -paramiko==3.4.1 -parso==0.8.3 -pexpect==4.8.0 -pg8000==1.29.8 -pgsu==0.3.0 -pgtest==1.3.2 -pickleshare==0.7.5 -pillow==9.5.0 -platformdirs==3.6.0 -plotly==5.15.0 -pluggy==1.0.0 -plumpy==0.22.3 -prometheus-client==0.17.0 -prompt-toolkit==3.0.38 -psutil==5.9.5 -psycopg[binary]==3.1.18 -ptyprocess==0.7.0 -pure-eval==0.2.2 -py-cpuinfo==9.0.0 -pybtex==0.24.0 -pycifrw==4.4.5 -pycparser==2.21 -pydantic==2.4.0 -pydantic-core==2.10.0 -pydata-sphinx-theme==0.15.1 -pygments==2.15.1 -pymatgen==2023.9.25 -pympler==1.0.1 -pymysql==0.9.3 -pynacl==1.5.0 -pyparsing==3.1.1 -pyrsistent==0.19.3 -pytest==7.3.2 -pytest-asyncio==0.16.0 -pytest-benchmark==4.0.0 -pytest-cov==4.1.0 -pytest-datadir==1.4.1 -pytest-regressions==2.4.2 -pytest-rerunfailures==12.0 -pytest-timeout==2.2.0 -python-dateutil==2.8.2 -python-json-logger==2.0.7 -python-memcached==1.59 -pytray==0.3.4 -pytz==2021.3 -pyyaml==6.0 -pyzmq==25.1.0 -qtconsole==5.4.3 -qtpy==2.3.1 -requests==2.31.0 -rfc3339-validator==0.1.4 -rfc3986-validator==0.1.1 -ruamel-yaml==0.17.32 -ruamel-yaml-clib==0.2.7 -scipy==1.10.1 -scramp==1.4.4 -seekpath==1.9.7 -send2trash==1.8.2 -shortuuid==1.0.11 -six==1.16.0 -sniffio==1.3.0 -snowballstemmer==2.2.0 -soupsieve==2.4.1 -spglib==2.0.2 -sphinx==7.2.6 -sphinx-copybutton==0.5.2 -sphinx-design==0.5.0 -sphinx-intl==2.1.0 -sphinx-notfound-page==1.0.0 -sphinx-sqlalchemy==0.2.0 -sphinxcontrib-applehelp==1.0.4 -sphinxcontrib-devhelp==1.0.2 -sphinxcontrib-htmlhelp==2.0.1 -sphinxcontrib-jsmath==1.0.1 -sphinxcontrib-qthelp==1.0.3 -sphinxcontrib-serializinghtml==1.1.9 -sphinxext-rediraffe==0.2.7 -sqlalchemy==2.0.23 -stack-data==0.6.2 -sympy==1.12 -tabulate==0.9.0 -tenacity==8.2.2 -terminado==0.17.1 -tinycss2==1.2.1 -tomli==2.0.1 -tornado==6.3.2 -tqdm==4.65.0 -traitlets==5.9.0 -typing-extensions==4.6.3 -tzdata==2023.3 -uncertainties==3.1.7 -upf-to-json==0.9.5 -urllib3==2.0.3 -wcwidth==0.2.6 -webencodings==0.5.1 -websocket-client==1.6.0 -werkzeug==2.3.6 -widgetsnbextension==4.0.7 -wrapt==1.15.0 -yarl==1.9.2 -zipp==3.15.0 - -# The following packages are considered to be unsafe in a requirements file: -# setuptools From 954b0cef928221635c6c5e96fc9351063374aecf Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Thu, 28 Nov 2024 19:25:33 +0000 Subject: [PATCH 06/15] Validate lockfile in CI --- .github/actions/install-aiida-core/action.yml | 4 +- .github/workflows/test-install.yml | 18 ++- .pre-commit-config.yaml | 6 +- utils/dependency_management.py | 108 ------------------ utils/validate_consistency.py | 9 +- 5 files changed, 18 insertions(+), 127 deletions(-) diff --git a/.github/actions/install-aiida-core/action.yml b/.github/actions/install-aiida-core/action.yml index aae701b540..578c5c9a5f 100644 --- a/.github/actions/install-aiida-core/action.yml +++ b/.github/actions/install-aiida-core/action.yml @@ -26,9 +26,9 @@ runs: python-version: ${{ inputs.python-version }} - name: Set up uv - uses: astral-sh/setup-uv@v3 + uses: astral-sh/setup-uv@v4 with: - version: 0.5.4 + version: 0.5.5 - name: Install dependencies from uv lock if: ${{ inputs.from-lock == 'true' }} diff --git a/.github/workflows/test-install.yml b/.github/workflows/test-install.yml index 7b8bc447b8..fd550b6ae0 100644 --- a/.github/workflows/test-install.yml +++ b/.github/workflows/test-install.yml @@ -30,18 +30,24 @@ jobs: steps: - uses: actions/checkout@v4 - - name: Set up Python 3.9 + - name: Set up Python 3.11 uses: actions/setup-python@v5 with: python-version: '3.9' + - name: Set up uv + uses: astral-sh/setup-uv@v4 + with: + version: 0.5.5 + - name: Install utils/ dependencies - run: pip install -r utils/requirements.txt + run: uv pip install --system -r utils/requirements.txt - - name: Validate - run: | - python ./utils/dependency_management.py check-requirements - python ./utils/dependency_management.py validate-all + - name: Validate uv lockfile + run: uv lock --locked + + - name: Validate conda environment file + run: python ./utils/dependency_management.py validate-environment-yml resolve-pip-dependencies: # Check whether the environments defined in the requirements/* files are diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 7a88a2ab99..88859a6f01 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -194,9 +194,9 @@ repos: src/aiida/workflows/arithmetic/multiply_add.py| )$ - - id: dm-generate-all - name: Update all requirements files - entry: python ./utils/dependency_management.py generate-all + - id: generate-environment-yml + name: Update conda environment file + entry: python ./utils/dependency_management.py generate-environment-yml language: system pass_filenames: false files: >- diff --git a/utils/dependency_management.py b/utils/dependency_management.py index dd6875e57e..aa15a6e3db 100755 --- a/utils/dependency_management.py +++ b/utils/dependency_management.py @@ -21,8 +21,6 @@ import tomli import yaml from packaging.requirements import Requirement -from packaging.specifiers import Specifier -from packaging.utils import canonicalize_name from packaging.version import parse ROOT = Path(__file__).resolve().parent.parent # repository root @@ -154,13 +152,6 @@ def generate_environment_yml(): ) -@cli.command() -@click.pass_context -def generate_all(ctx): - """Generate all dependent requirement files.""" - ctx.invoke(generate_environment_yml) - - @cli.command('validate-environment-yml', help="Validate 'environment.yml'.") def validate_environment_yml(): """Validate that 'environment.yml' is consistent with 'pyproject.toml'.""" @@ -235,105 +226,6 @@ def validate_environment_yml(): click.secho('Conda dependency specification is consistent.', fg='green') -@cli.command('validate-all', help='Validate consistency of all requirements.') -@click.pass_context -def validate_all(ctx): - """Validate consistency of all requirement specifications of the package. - - Validates that the specification of requirements/dependencies is consistent across - the following files: - - - pyproject.toml - - environment.yml - - """ - ctx.invoke(validate_environment_yml) - - -@cli.command() -@click.argument('extras', nargs=-1) -@click.option( - '--github-annotate/--no-github-annotate', - default=True, - hidden=True, - help='Control whether to annotate files with context-specific warnings ' - 'as part of a GitHub actions workflow. Note: Requires environment ' - 'variable GITHUB_ACTIONS=true .', -) -def check_requirements(extras, github_annotate): - """Check the 'requirements/*.txt' files. - - Checks that the environments specified in the requirements files - match all the dependencies specified in 'pyproject.toml'. - - The arguments allow to specify which 'extra' requirements to expect. - Use 'DEFAULT' to select 'atomic_tools', 'docs', 'notebook', 'rest', and 'tests'. - - """ - if len(extras) == 1 and extras[0] == 'DEFAULT': - extras = ['atomic_tools', 'docs', 'notebook', 'rest', 'tests'] - - # Read the requirements from 'pyproject.toml'' - pyproject = _load_pyproject() - install_requires = pyproject['project']['dependencies'] - for extra in extras: - install_requires.extend(pyproject['project']['optional-dependencies'][extra]) - install_requires = set(parse_requirements(install_requires)) - - not_installed = defaultdict(list) - for fn_req in (ROOT / 'requirements').iterdir(): - match = re.match(r'.*-py-(.*)\.txt', str(fn_req)) - if not match: - continue - env = {'python_version': match.groups()[0]} - requirements_abstract = {r for r in install_requires if r.marker is None or r.marker.evaluate(env)} - installed = [] - - with open(fn_req, encoding='utf8') as req_file: - requirements_concrete = parse_requirements(req_file) - - for requirement_abstract in requirements_abstract: - for requirement_concrete in requirements_concrete: - version = Specifier(str(requirement_concrete.specifier)).version - if canonicalize_name(requirement_abstract.name) == canonicalize_name( - requirement_concrete.name - ) and requirement_abstract.specifier.contains(version): - installed.append(requirement_abstract) - break - - for dependency in requirements_abstract.difference(set(installed)): - not_installed[dependency].append(fn_req) - - if any(not_installed.values()): - setup_json_linenos = _find_linenos_of_requirements_in_pyproject(not_installed) - - # Format error message to be presented to user. - error_msg = ["The requirements/ files are missing dependencies specified in the 'pyproject.toml' file.", ''] - for dependency, fn_reqs in not_installed.items(): - src = 'pyproject.toml' + ','.join(str(lineno + 1) for lineno in setup_json_linenos[dependency]) - error_msg.append(f'{src}: No match for dependency `{dependency}` in:') - for fn_req in sorted(fn_reqs): - error_msg.append(f' - {fn_req.relative_to(ROOT)}') - - if GITHUB_ACTIONS: - # Set the step ouput error message which can be used, e.g., for display as part of an issue comment. - print('::set-output name=error::' + '%0A'.join(error_msg)) - - if GITHUB_ACTIONS and github_annotate: - # Annotate the pyproject.toml' file with specific warnings. - for dependency, fn_reqs in not_installed.items(): - for lineno in setup_json_linenos[dependency]: - print( - f'::warning file=pyproject.toml,line={lineno+1}::' - f"No match for dependency '{dependency}' in: " - + ','.join(str(fn_req.relative_to(ROOT)) for fn_req in fn_reqs) - ) - - raise DependencySpecificationError('\n'.join(error_msg)) - - click.secho("Requirements files appear to be in sync with specifications in 'pyproject.toml''.", fg='green') - - @cli.command() @click.argument('extras', nargs=-1) @click.option('--format', 'fmt', type=click.Choice(['pip', 'pipfile']), default='pip') diff --git a/utils/validate_consistency.py b/utils/validate_consistency.py index 297dfccab8..0e4070491c 100644 --- a/utils/validate_consistency.py +++ b/utils/validate_consistency.py @@ -7,14 +7,7 @@ # For further information on the license, see the LICENSE.txt file # # For further information please visit http://www.aiida.net # ########################################################################### -"""Validate consistency of versions and dependencies. - -Validates consistency of - - * pyproject.toml - * environment.yml - -""" +"""Autogenerate verdi CLI documentation from click.""" import os From 166c9786751fcef4e984032d1ab9217babf9c7c3 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Thu, 28 Nov 2024 19:27:56 +0000 Subject: [PATCH 07/15] Add pre-commit hook for checking uv lockfile In this implementation, the hook will only check whether the lockfile is compatible with pyproject.toml, it will not try to automatically update it, since that should be decided by the developer. --- .pre-commit-config.yaml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 88859a6f01..145bc6f01c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -194,6 +194,17 @@ repos: src/aiida/workflows/arithmetic/multiply_add.py| )$ + - id: check-uv-lock + name: Check uv lockfile up to date + # NOTE: This will not automatically update the lockfile + entry: uv lock --locked + language: system + pass_filenames: false + files: >- + (?x)^( + pyproject.toml| + )$ + - id: generate-environment-yml name: Update conda environment file entry: python ./utils/dependency_management.py generate-environment-yml From b0cadafd732e76fd2fcc1275931b8a60c671aa28 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Thu, 28 Nov 2024 19:46:25 +0000 Subject: [PATCH 08/15] Fix pre-commit config --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 145bc6f01c..d222449f52 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ ci: autofix_prs: true autoupdate_commit_msg: 'Devops: Update pre-commit dependencies' autoupdate_schedule: quarterly - skip: [mypy, dm-generate-all, dependencies, verdi-autodocs] + skip: [mypy, check-uv-lock, generate-conda-environment, validate-conda-environment, verdi-autodocs] repos: - repo: https://github.com/pre-commit/pre-commit-hooks @@ -205,7 +205,7 @@ repos: pyproject.toml| )$ - - id: generate-environment-yml + - id: generate-conda-environment name: Update conda environment file entry: python ./utils/dependency_management.py generate-environment-yml language: system @@ -216,7 +216,7 @@ repos: utils/dependency_management.py )$ - - id: dependencies + - id: validate-conda-environment name: Validate environment.yml entry: python ./utils/dependency_management.py validate-environment-yml language: system From 3517d65412bfff6a210b2da17bd3cdb7c4b2e23c Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Thu, 28 Nov 2024 19:47:57 +0000 Subject: [PATCH 09/15] Remove check-requirements job --- .github/actions/install-aiida-core/action.yml | 1 + .github/workflows/ci-code.yml | 31 ------------------- 2 files changed, 1 insertion(+), 31 deletions(-) diff --git a/.github/actions/install-aiida-core/action.yml b/.github/actions/install-aiida-core/action.yml index 578c5c9a5f..f44b6b7262 100644 --- a/.github/actions/install-aiida-core/action.yml +++ b/.github/actions/install-aiida-core/action.yml @@ -31,6 +31,7 @@ runs: version: 0.5.5 - name: Install dependencies from uv lock + # NOTE: We're also asserting that the lockfile is up to date if: ${{ inputs.from-lock == 'true' }} run: uv sync --locked --extra pre-commit shell: bash diff --git a/.github/workflows/ci-code.yml b/.github/workflows/ci-code.yml index 8ae362e0c7..fe1d1dbc41 100644 --- a/.github/workflows/ci-code.yml +++ b/.github/workflows/ci-code.yml @@ -18,37 +18,6 @@ env: jobs: - check-requirements: - - runs-on: ubuntu-latest - timeout-minutes: 5 - - steps: - - uses: actions/checkout@v4 - - - name: Set up Python 3.12 - uses: actions/setup-python@v5 - with: - python-version: '3.12' - - - name: Install utils/ dependencies - run: pip install -r utils/requirements.txt - - # TODO: Change this to make sure that the lock is up-to-date - - name: Check requirements files - id: check_reqs - run: python ./utils/dependency_management.py check-requirements DEFAULT - - - name: Create commit comment - if: failure() && steps.check_reqs.outputs.error - uses: peter-evans/commit-comment@v3 - with: - path: pyproject.toml - body: | - ${{ steps.check_reqs.outputs.error }} - - Click [here](https://github.com/aiidateam/aiida-core/wiki/AiiDA-Dependency-Management) for more information on dependency management. - tests: needs: [check-requirements] From e3fb04dda5d256a110d56b5584734d285020653b Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Thu, 28 Nov 2024 20:20:04 +0000 Subject: [PATCH 10/15] Update CODEOWNERS file --- .github/CODEOWNERS | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index e908ba2fc9..74ecd660e8 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -2,9 +2,7 @@ # currently active dependency manager (DM) to trigger an automatic review # request from the DM upon changes. Please see AEP-002 for details: # https://github.com/aiidateam/AEP/tree/master/002_dependency_management -setup.* @aiidateam/dependency-manager environment.yml @aiidateam/dependency-manager -requirements*.txt @aiidateam/dependency-manager pyproject.toml @aiidateam/dependency-manager +uv.lock @aiidateam/dependency-manager utils/dependency_management.py @aiidateam/dependency-manager -.github/workflows/dm.yml @aiidateam/dependency-manager From 10cd62a7742e12e4ba2d7cbff5566016d625989c Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Thu, 28 Nov 2024 20:32:11 +0000 Subject: [PATCH 11/15] CI: Remove needless jobs --- .github/workflows/ci-code.yml | 4 - .github/workflows/test-install.yml | 138 +---------------------------- 2 files changed, 1 insertion(+), 141 deletions(-) diff --git a/.github/workflows/ci-code.yml b/.github/workflows/ci-code.yml index fe1d1dbc41..6fc31c3c7b 100644 --- a/.github/workflows/ci-code.yml +++ b/.github/workflows/ci-code.yml @@ -20,8 +20,6 @@ jobs: tests: - needs: [check-requirements] - runs-on: ubuntu-latest timeout-minutes: 45 @@ -88,7 +86,6 @@ jobs: tests-presto: - needs: [check-requirements] runs-on: ubuntu-latest timeout-minutes: 20 @@ -114,7 +111,6 @@ jobs: verdi: - needs: [check-requirements] runs-on: ubuntu-latest timeout-minutes: 10 diff --git a/.github/workflows/test-install.yml b/.github/workflows/test-install.yml index fd550b6ae0..cd9849ebb3 100644 --- a/.github/workflows/test-install.yml +++ b/.github/workflows/test-install.yml @@ -4,7 +4,6 @@ on: pull_request: paths: - environment.yml - - '**/requirements*.txt' - pyproject.toml - util/dependency_management.py - .github/workflows/test-install.yml @@ -14,7 +13,7 @@ on: # https://docs.github.com/en/actions/using-jobs/using-concurrency concurrency: - # only cancel in-progress jobs or runs for the current workflow - matches against branch & tags + # only cancel in-progress jobs or runs for the current workflow - matches against branch & tags group: ${{ github.workflow }}-${{ github.ref }} cancel-in-progress: true @@ -49,32 +48,6 @@ jobs: - name: Validate conda environment file run: python ./utils/dependency_management.py validate-environment-yml - resolve-pip-dependencies: - # Check whether the environments defined in the requirements/* files are - # resolvable. - - needs: [validate-dependency-specification] - if: github.repository == 'aiidateam/aiida-core' - runs-on: ubuntu-latest - timeout-minutes: 5 - - strategy: - fail-fast: false - matrix: - python-version: ['3.9', '3.10', '3.11', '3.12'] - - steps: - - uses: actions/checkout@v4 - - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v5 - with: - python-version: ${{ matrix.python-version }} - - - name: Resolve dependencies from requirements file. - run: | - pip install --dry-run --ignore-installed -r requirements/requirements-py-${{ matrix.python-version }}.txt - create-conda-environment: # Verify that we can create a valid conda environment from the environment.yml file. @@ -236,112 +209,3 @@ jobs: AIIDA_TEST_PROFILE: test_aiida AIIDA_WARN_v3: 1 run: pytest --db-backend psql tests -m 'not nightly' tests/ - - - name: Freeze test environment - run: pip freeze | sed '1d' | tee requirements-py-${{ matrix.python-version }}.txt - - # Add python-version specific requirements/ file to the requirements.txt artifact. - # This artifact can be used in the next step to automatically create a pull request - # updating the requirements (in case they are inconsistent with the pyproject.toml file). - - uses: actions/upload-artifact@v4 - with: - name: requirements-py-${{ matrix.python-version }}.txt - path: requirements-py-${{ matrix.python-version }}.txt - -# Check whether the requirements/ files are consistent with the dependency specification in the pyproject.toml file. -# If the check fails, warn the user via a comment and try to automatically create a pull request to update the files -# (does not work on pull requests from forks). - - check-requirements: - - needs: tests - - runs-on: ubuntu-latest - timeout-minutes: 5 - - steps: - - uses: actions/checkout@v4 - - - name: Set up Python 3.9 - uses: actions/setup-python@v5 - with: - python-version: 3.9 - - - name: Install utils/ dependencies - run: pip install -r utils/requirements.txt - - - name: Check consistency of requirements/ files - id: check_reqs - continue-on-error: true - run: python ./utils/dependency_management.py check-requirements DEFAULT --no-github-annotate - -# -# The following steps are only executed if the consistency check failed. -# - - name: Create commit comment - if: steps.check_reqs.outcome == 'Failure' # only run if requirements/ are inconsistent - uses: peter-evans/commit-comment@v3 - with: - token: ${{ secrets.GITHUB_TOKEN }} - path: pyproject.toml - body: | - The requirements/ files are inconsistent! - - # Check out the base branch so that we can prepare the pull request. - - name: Checkout base branch - if: steps.check_reqs.outcome == 'Failure' # only run if requirements/ are inconsistent - uses: actions/checkout@v4 - with: - ref: ${{ github.head_ref }} - clean: true - - - name: Download requirements.txt files - if: steps.check_reqs.outcome == 'Failure' # only run if requirements/ are inconsistent - uses: actions/download-artifact@v4 - with: - pattern: requirements-py-* - merge-multiple: true - path: requirements - - - name: Commit requirements files - if: steps.check_reqs.outcome == 'Failure' # only run if requirements/ are inconsistent - run: | - git add requirements/* - - - name: Create pull request for updated requirements files - if: steps.check_reqs.outcome == 'Failure' # only run if requirements/ are inconsistent - id: create_update_requirements_pr - continue-on-error: true - uses: peter-evans/create-pull-request@v7 - with: - branch: update-requirements - commit-message: Automated update of requirements/ files. - title: Update requirements/ files. - body: | - Update requirements files to ensure that they are consistent - with the dependencies specified in the 'pyproject.toml' file. - - Please note, that this pull request was likely created to - resolve the inconsistency for a specific dependency, however - other versions that have changed since the last update will - be included as part of this commit as well. - - Click [here](https://github.com/aiidateam/aiida-core/wiki/AiiDA-Dependency-Management) for more information. - - - name: Create PR comment on success - if: steps.create_update_requirements_pr.outcome == 'Success' - uses: peter-evans/create-or-update-comment@v4 - with: - issue-number: ${{ github.event.number }} - body: | - I automatically created a pull request (#${{ steps.create_update_requirements_pr.outputs.pr_number }}) that adapts the - requirements/ files according to the dependencies specified in the 'pyproject.toml' file. - - - name: Create PR comment on failure - if: steps.create_update_requirements_pr.outcome == 'Failure' - uses: peter-evans/create-or-update-comment@v4 - with: - issue-number: ${{ github.event.number }} - body: | - Please update the requirements/ files to ensure that they - are consistent with the dependencies specified in the 'pyproject.toml' file. From c5c63a2d6a1b1830206670adf4470660b9419504 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Mon, 2 Dec 2024 12:11:41 +0000 Subject: [PATCH 12/15] Update lock --- uv.lock | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/uv.lock b/uv.lock index 0230272b77..01493fe251 100644 --- a/uv.lock +++ b/uv.lock @@ -109,6 +109,7 @@ pre-commit = [ { name = "pytest-regressions" }, { name = "pytest-rerunfailures" }, { name = "pytest-timeout" }, + { name = "pytest-xdist" }, { name = "python-memcached" }, { name = "seekpath" }, { name = "spglib" }, @@ -144,6 +145,7 @@ tests = [ { name = "pytest-regressions" }, { name = "pytest-rerunfailures" }, { name = "pytest-timeout" }, + { name = "pytest-xdist" }, { name = "sphinx" }, ] tui = [ @@ -207,6 +209,7 @@ requires-dist = [ { name = "pytest-regressions", marker = "extra == 'tests'", specifier = "~=2.2" }, { name = "pytest-rerunfailures", marker = "extra == 'tests'", specifier = "~=12.0" }, { name = "pytest-timeout", marker = "extra == 'tests'", specifier = "~=2.0" }, + { name = "pytest-xdist", marker = "extra == 'tests'", specifier = "~=3.6" }, { name = "python-memcached", marker = "extra == 'rest'", specifier = "~=1.59" }, { name = "pytz", specifier = "~=2021.1" }, { name = "pyyaml", specifier = "~=6.0" }, @@ -1134,6 +1137,15 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/02/cc/b7e31358aac6ed1ef2bb790a9746ac2c69bcb3c8588b41616914eb106eaf/exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b", size = 16453 }, ] +[[package]] +name = "execnet" +version = "2.1.1" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/bb/ff/b4c0dc78fbe20c3e59c0c7334de0c27eb4001a2b2017999af398bf730817/execnet-2.1.1.tar.gz", hash = "sha256:5189b52c6121c24feae288166ab41b32549c7e2348652736540b9e6e7d4e72e3", size = 166524 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/43/09/2aea36ff60d16dd8879bdb2f5b3ee0ba8d08cbbdcdfe870e695ce3784385/execnet-2.1.1-py3-none-any.whl", hash = "sha256:26dee51f1b80cebd6d0ca8e74dd8745419761d3bef34163928cbebbdc4749fdc", size = 40612 }, +] + [[package]] name = "executing" version = "2.1.0" @@ -3555,6 +3567,19 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/03/27/14af9ef8321f5edc7527e47def2a21d8118c6f329a9342cc61387a0c0599/pytest_timeout-2.3.1-py3-none-any.whl", hash = "sha256:68188cb703edfc6a18fad98dc25a3c61e9f24d644b0b70f33af545219fc7813e", size = 14148 }, ] +[[package]] +name = "pytest-xdist" +version = "3.6.1" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "execnet" }, + { name = "pytest" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/41/c4/3c310a19bc1f1e9ef50075582652673ef2bfc8cd62afef9585683821902f/pytest_xdist-3.6.1.tar.gz", hash = "sha256:ead156a4db231eec769737f57668ef58a2084a34b2e55c4a8fa20d861107300d", size = 84060 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/6d/82/1d96bf03ee4c0fdc3c0cbe61470070e659ca78dc0086fb88b66c185e2449/pytest_xdist-3.6.1-py3-none-any.whl", hash = "sha256:9ed4adfb68a016610848639bb7e02c9352d5d9f03d04809919e2dafc3be4cca7", size = 46108 }, +] + [[package]] name = "python-dateutil" version = "2.9.0.post0" From 352539d1c3eaa078d003e3466c84c948e0a3cfc3 Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Mon, 2 Dec 2024 12:19:56 +0000 Subject: [PATCH 13/15] Update CODEOWNERS --- .github/CODEOWNERS | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 74ecd660e8..3b1e3cb611 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -2,7 +2,7 @@ # currently active dependency manager (DM) to trigger an automatic review # request from the DM upon changes. Please see AEP-002 for details: # https://github.com/aiidateam/AEP/tree/master/002_dependency_management -environment.yml @aiidateam/dependency-manager -pyproject.toml @aiidateam/dependency-manager -uv.lock @aiidateam/dependency-manager -utils/dependency_management.py @aiidateam/dependency-manager +environment.yml @unkcpz @agoscinski +pyproject.toml @unkcpz @agoscinski +uv.lock @unkcpz @agoscinski +utils/dependency_management.py @unkcpz @agoscinski From 7959c4dc39524143e6caa2d5cee0591b89aba85c Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 4 Dec 2024 11:49:38 +0000 Subject: [PATCH 14/15] Add comments --- .github/actions/install-aiida-core/action.yml | 7 ++++++- .github/workflows/ci-code.yml | 1 + 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/actions/install-aiida-core/action.yml b/.github/actions/install-aiida-core/action.yml index f44b6b7262..ac77549d15 100644 --- a/.github/actions/install-aiida-core/action.yml +++ b/.github/actions/install-aiida-core/action.yml @@ -12,6 +12,9 @@ inputs: required: false # NOTE: Hard-learned lesson: we cannot use type=boolean here, apparently :-( # https://stackoverflow.com/a/76294014 + # NOTE2: When installing from lockfile, aiida-core and its dependencies + # are installed in a virtual environment located in .venv directory. + # Subsuquent jobs steps must either activate the environment or use `uv run` from-lock: description: Install aiida-core dependencies from a uv lock file default: 'true' @@ -31,8 +34,10 @@ runs: version: 0.5.5 - name: Install dependencies from uv lock - # NOTE: We're also asserting that the lockfile is up to date if: ${{ inputs.from-lock == 'true' }} + # NOTE: We're asserting that the lockfile is up to date + # NOTE2: 'pre-commit' extra recursively contains other extras + # needed to run the tests. run: uv sync --locked --extra pre-commit shell: bash diff --git a/.github/workflows/ci-code.yml b/.github/workflows/ci-code.yml index 346910a7b7..8346d9fdea 100644 --- a/.github/workflows/ci-code.yml +++ b/.github/workflows/ci-code.yml @@ -64,6 +64,7 @@ jobs: python-version: ${{ matrix.python-version }} - name: Setup environment + # Note: The virtual environment in .venv was created by uv in previous step run: source .venv/bin/activate && .github/workflows/setup.sh - name: Run test suite From e62a2ef9810155858049c879d1d78876cd80aace Mon Sep 17 00:00:00 2001 From: Daniel Hollas Date: Wed, 4 Dec 2024 11:51:52 +0000 Subject: [PATCH 15/15] Bump uv version --- .github/actions/install-aiida-core/action.yml | 2 +- .github/workflows/test-install.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/actions/install-aiida-core/action.yml b/.github/actions/install-aiida-core/action.yml index ac77549d15..01cadce940 100644 --- a/.github/actions/install-aiida-core/action.yml +++ b/.github/actions/install-aiida-core/action.yml @@ -31,7 +31,7 @@ runs: - name: Set up uv uses: astral-sh/setup-uv@v4 with: - version: 0.5.5 + version: 0.5.6 - name: Install dependencies from uv lock if: ${{ inputs.from-lock == 'true' }} diff --git a/.github/workflows/test-install.yml b/.github/workflows/test-install.yml index 6d5c4f52d7..7a0076fbbd 100644 --- a/.github/workflows/test-install.yml +++ b/.github/workflows/test-install.yml @@ -37,7 +37,7 @@ jobs: - name: Set up uv uses: astral-sh/setup-uv@v4 with: - version: 0.5.5 + version: 0.5.6 - name: Install utils/ dependencies run: uv pip install --system -r utils/requirements.txt