diff --git a/.flake8 b/.flake8 new file mode 100644 index 0000000..10b08c8 --- /dev/null +++ b/.flake8 @@ -0,0 +1,4 @@ +[flake8] +exclude = .git, .venv* +max-line-length = 120 +max-complexity = 10 \ No newline at end of file diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 993256a..50f1998 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -19,24 +19,56 @@ jobs: python-version: ["3.9", "3.10", "3.11"] steps: - - uses: actions/checkout@v2 - with: - submodules: 'recursive' - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v3 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - python -m pip install flake8 pytest - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - name: Test with pytest - run: | - pytest + - uses: actions/checkout@v2 + with: + submodules: 'recursive' + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v3 + with: + python-version: ${{ matrix.python-version }} + + # Cache the installation of Poetry itself, e.g. the next step. This prevents the workflow + # from installing Poetry every time, which can be slow. Note the use of the Poetry version + # number in the cache key, and the "-0" suffix: this allows you to invalidate the cache + # manually if/when you want to upgrade Poetry, or if something goes wrong. + - name: Cache poetry + uses: actions/cache@v3.3.2 + with: + path: ~/.local + key: poetry-1.7.1-0 + + - name: Install peotry + uses: snok/install-poetry@v1 + with: + version: 1.7.1 + virtualenvs-create: true + virtualenvs-in-project: true + + - run: poetry --version + + # Cache your dependencies (i.e. all the stuff in your `pyproject.toml`). Note the cache + # key: if you're using multiple Python versions, or multiple OSes, you'd need to include + # them in the cache key. I'm not, so it can be simple and just depend on the poetry.lock. + - name: Cache dependencies + id: cache-deps + uses: actions/cache@v3.3.2 + with: + path: .venv + key: pydeps-${{ hashFiles('**/poetry.lock') }} + + - name: Install dependencies + # `--no-root` means "install all dependencies but not the project itself" + # The `if` statement ensures this only runs on a cache miss. + run: poetry install --no-interaction --no-root + if: steps.cache-deps.outputs.cache-hit != 'true' + + - name: Lint with flake8 + run: | + # stop the build if there are Python syntax errors or undefined names + poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + + - name: Test with pytest + run: poetry run pytest diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..261eeb9 --- /dev/null +++ b/LICENSE @@ -0,0 +1,201 @@ + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README.md b/README.md index 845dbbb..4821abe 100644 --- a/README.md +++ b/README.md @@ -24,25 +24,17 @@ git submodule update ``` -## Python virtual environment +## Dependency management with Poetry -```bash -python3 -m venv .venv -source .venv/bin/activate -... DO YOUR WORK ... -deactivate -``` - - -## Conda environment - -Based on [Miniconda](https://docs.conda.io/en/latest/miniconda.html) all dependencies can be installed in a conda environment. The environment can be created and activated with the following commands: +Based on [Poerty](https://python-poetry.org/) all dependencies can be installed in a virtual environment. The environment can be created and activated with the following commands: ```bash -conda env create -conda activate spherinator +poetry install --no-root +poerty shell ``` +The `--no-root` option is used to avoid installing the project itself as a dependency. The environment can be deactivated with `exit`. + ## LightningCLI @@ -89,3 +81,8 @@ python spherinator.sh fit -c experiments/illustris_power.yaml \ -c experiments/wandb.yaml \ -c experiments/callback_log_reconstructions.yaml ``` + + +## License + +This project is licensed under the [Apache-2.0 License](http://www.apache.org/licenses/LICENSE-2.0). diff --git a/environment.yml b/environment.yml deleted file mode 100644 index 5eb45c5..0000000 --- a/environment.yml +++ /dev/null @@ -1,25 +0,0 @@ -name: spherinator -channels: - - conda-forge -dependencies: - - healpy==1.16.5 - - jupytext==1.15.1 - - lightning==2.0.9 - - matplotlib==3.7.2 - - numpy==1.25.2 - - onnx==1.14.1 - - onnxruntime==1.15.1 - - pandas==2.1.0 - - pip==23.2.1 - - python==3.10.12 - - pytorch-gpu==2.0.0 - - scikit-image==0.21.0 - - scikit-learn==1.3.0 - - scipy==1.11.2 - - torchvision==0.15.2 - - wandb==0.15.10 - - pip: - - ipykernel==6.25.2 - - jsonargparse[signatures]==4.24.1 - - tensorboard==2.14.0 - - 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(>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] + +[metadata] +lock-version = "2.0" +python-versions = "^3.9" +content-hash = "c55ab7337b5c357fd67c839d36df9395df5de1d50402aec3260b06af881c32f0" diff --git a/pyproject.toml b/pyproject.toml index cbda5e8..8e3dc8e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,47 @@ +[tool.poetry] +name = "spherinator" +version = "0.1.0" +description = "Rotation-Invariant Hyperspherical Variational Convolutional Autoencoder" +authors = [ + "Kai Polsterer ", + "Bernd Doser ", + "Andreas Fehlner ", + "Sebastian T. Gomez ", +] +license = "Apache-2.0" +readme = "README.md" + +[tool.poetry.dependencies] +astropy = "5.3.4" +lightning = "2.1.2" +matplotlib = "3.8.2" +python = "^3.9" +scikit-image = "0.22.0" +scipy = "1.11.4" +torch = "2.1.1" +torchvision = "0.16.1" + +[tool.poetry.group.dev.dependencies] +flake8 = "6.1.0" +healpy = "1.16.6" +ipykernel = "6.26.0" +jsonargparse = "4.27.0" +jupytext = "1.15.2" +numpy = "1.26.2" +onnx = "1.15.0" +onnxruntime = "1.16.3" +pandas = "2.1.3" +pip-licenses = "4.3.3" +pytest = "7.4.3" +pytest-cov = "4.1.0" +scikit-learn = "1.3.2" +tensorboard = "2.15.1" +wandb = "0.16.0" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + [tool.pytest] timeout = 300 testpaths = 'tests' diff --git a/requirements-dev.in b/requirements-dev.in deleted file mode 100644 index 5f47e00..0000000 --- a/requirements-dev.in +++ /dev/null @@ -1,22 +0,0 @@ -astropy==5.3.4 -healpy==1.16.6 -ipykernel==6.26.0 -jsonargparse[signatures]==4.27.0 -jupytext==1.15.2 -lightning==2.1.2 -matplotlib==3.8.2 -numpy==1.26.2 -onnx==1.15.0 -onnxruntime==1.16.3 -pandas==2.1.3 -pytest-cov==4.1.0 -pytest==7.4.3 -pip-licenses==4.3.3 -scikit-image==0.22.0 -scikit-learn==1.3.2 -scipy==1.11.4 -tensorboard==2.15.1 -tensorrt==8.6.1.post1 -torch==2.1.1 -torchvision==0.16.1 -wandb==0.16.0 diff --git a/requirements-dev.txt b/requirements-dev.txt deleted file mode 100644 index 0ddbec8..0000000 --- a/requirements-dev.txt +++ /dev/null @@ -1,462 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.9 -# by the following command: -# -# pip-compile requirements-dev.in -# -absl-py==2.0.0 - # via tensorboard -aiohttp==3.9.0 - # via fsspec -aiosignal==1.3.1 - # via aiohttp -appdirs==1.4.4 - # via wandb -astropy==5.3.4 - # via - # -r requirements-dev.in - # healpy -asttokens==2.4.1 - # via stack-data -async-timeout==4.0.3 - # via aiohttp -attrs==23.1.0 - # via - # aiohttp - # jsonschema - # referencing -cachetools==5.3.2 - # via google-auth -certifi==2023.11.17 - # via - # requests - # sentry-sdk -charset-normalizer==3.3.2 - # via requests -click==8.1.7 - # via wandb -coloredlogs==15.0.1 - # via onnxruntime -comm==0.2.0 - # via ipykernel -contourpy==1.2.0 - # via matplotlib -coverage[toml]==7.3.2 - # via - # coverage - # pytest-cov -cycler==0.12.1 - # via matplotlib -debugpy==1.8.0 - # via ipykernel -decorator==5.1.1 - # via ipython -docker-pycreds==0.4.0 - # via wandb -docstring-parser==0.15 - # via jsonargparse -exceptiongroup==1.2.0 - # via - # ipython - # pytest -executing==2.0.1 - # via stack-data -fastjsonschema==2.19.0 - # via nbformat -filelock==3.13.1 - # via - # torch - # triton -flatbuffers==23.5.26 - # via onnxruntime -fonttools==4.45.0 - # via matplotlib -frozenlist==1.4.0 - # via - # aiohttp - # aiosignal -fsspec[http]==2023.10.0 - # via - # fsspec - # lightning - # pytorch-lightning - # torch -gitdb==4.0.11 - # via gitpython -gitpython==3.1.40 - # via wandb -google-auth==2.23.4 - # via - # google-auth-oauthlib - # tensorboard -google-auth-oauthlib==1.1.0 - # via tensorboard -grpcio==1.59.3 - # via tensorboard -healpy==1.16.6 - # via -r requirements-dev.in -humanfriendly==10.0 - # via coloredlogs -idna==3.4 - # via - # requests - # yarl -imageio==2.33.0 - # via scikit-image -importlib-metadata==6.8.0 - # via - # jupyter-client - # markdown -importlib-resources==6.1.1 - # via - # matplotlib - # typeshed-client -iniconfig==2.0.0 - # via pytest -ipykernel==6.26.0 - # via -r requirements-dev.in -ipython==8.17.2 - # via ipykernel -jedi==0.19.1 - # via ipython -jinja2==3.1.2 - # via torch -joblib==1.3.2 - # via scikit-learn -jsonargparse[signatures,typing-extensions]==4.27.0 - # via - # -r requirements-dev.in - # jsonargparse -jsonschema==4.20.0 - # via nbformat -jsonschema-specifications==2023.11.1 - # via jsonschema -jupyter-client==8.6.0 - # via ipykernel -jupyter-core==5.5.0 - # via - # ipykernel - # jupyter-client - # nbformat -jupytext==1.15.2 - # via -r requirements-dev.in -kiwisolver==1.4.5 - # via matplotlib -lazy-loader==0.3 - # via scikit-image -lightning==2.1.2 - # via -r requirements-dev.in -lightning-utilities==0.10.0 - # via - # lightning - # pytorch-lightning - # torchmetrics -markdown==3.5.1 - # via tensorboard -markdown-it-py==3.0.0 - # via - # jupytext - # mdit-py-plugins -markupsafe==2.1.3 - # via - # jinja2 - # werkzeug -matplotlib==3.8.2 - # via - # -r requirements-dev.in - # healpy -matplotlib-inline==0.1.6 - # via - # ipykernel - # ipython -mdit-py-plugins==0.4.0 - # via jupytext -mdurl==0.1.2 - # via markdown-it-py -mpmath==1.3.0 - # via sympy -multidict==6.0.4 - # via - # aiohttp - # yarl -nbformat==5.9.2 - # via jupytext -nest-asyncio==1.5.8 - # via ipykernel -networkx==3.2.1 - # via - # scikit-image - # torch -numpy==1.26.2 - # via - # -r requirements-dev.in - # astropy - # contourpy - # healpy - # imageio - # lightning - # matplotlib - # onnx - # onnxruntime - # pandas - # pyerfa - # pytorch-lightning - # scikit-image - # scikit-learn - # scipy - # tensorboard - # tifffile - # torchmetrics - # torchvision -nvidia-cublas-cu12==12.1.3.1 - # via - # nvidia-cudnn-cu12 - # nvidia-cusolver-cu12 - # torch -nvidia-cuda-cupti-cu12==12.1.105 - # via torch -nvidia-cuda-nvrtc-cu12==12.1.105 - # via torch -nvidia-cuda-runtime-cu12==12.1.105 - # via torch -nvidia-cudnn-cu12==8.9.2.26 - # via torch -nvidia-cufft-cu12==11.0.2.54 - # via torch -nvidia-curand-cu12==10.3.2.106 - # via torch -nvidia-cusolver-cu12==11.4.5.107 - # via torch -nvidia-cusparse-cu12==12.1.0.106 - # via - # nvidia-cusolver-cu12 - # torch -nvidia-nccl-cu12==2.18.1 - # via torch -nvidia-nvjitlink-cu12==12.3.101 - # via - # nvidia-cusolver-cu12 - # nvidia-cusparse-cu12 -nvidia-nvtx-cu12==12.1.105 - # via torch -oauthlib==3.2.2 - # via requests-oauthlib -onnx==1.15.0 - # via -r requirements-dev.in -onnxruntime==1.16.3 - # via -r requirements-dev.in -packaging==23.2 - # via - # astropy - # ipykernel - # lightning - # lightning-utilities - # matplotlib - # onnxruntime - # pytest - # pytorch-lightning - # scikit-image -pandas==2.1.3 - # via -r requirements-dev.in -parso==0.8.3 - # via jedi -pexpect==4.8.0 - # via ipython -pillow==10.1.0 - # via - # imageio - # matplotlib - # scikit-image - # torchvision -pip-licenses==4.3.3 - # via -r requirements-dev.in -platformdirs==4.0.0 - # via jupyter-core -pluggy==1.3.0 - # via pytest -prettytable==3.9.0 - # via pip-licenses -prompt-toolkit==3.0.41 - # via ipython -protobuf==4.23.4 - # via - # onnx - # onnxruntime - # tensorboard - # wandb -psutil==5.9.6 - # via - # ipykernel - # wandb -ptyprocess==0.7.0 - # via pexpect -pure-eval==0.2.2 - # via stack-data -pyasn1==0.5.1 - # via - # pyasn1-modules - # rsa -pyasn1-modules==0.3.0 - # via google-auth -pyerfa==2.0.1.1 - # via astropy -pygments==2.17.1 - # via ipython -pyparsing==3.0.9 - # via matplotlib -pytest==7.4.3 - # via - # -r requirements-dev.in - # pytest-cov -pytest-cov==4.1.0 - # via -r requirements-dev.in -python-dateutil==2.8.2 - # via - # jupyter-client - # matplotlib - # pandas -pytorch-lightning==2.1.2 - # via lightning -pytz==2023.3.post1 - # via pandas -pyyaml==6.0.1 - # via - # astropy - # jsonargparse - # jupytext - # lightning - # pytorch-lightning - # wandb -pyzmq==25.1.1 - # via - # ipykernel - # jupyter-client -referencing==0.31.0 - # via - # jsonschema - # jsonschema-specifications -requests==2.31.0 - # via - # fsspec - # requests-oauthlib - # tensorboard - # torchvision - # wandb -requests-oauthlib==1.3.1 - # via google-auth-oauthlib -rpds-py==0.13.1 - # via - # jsonschema - # referencing -rsa==4.9 - # via google-auth -scikit-image==0.22.0 - # via -r requirements-dev.in -scikit-learn==1.3.2 - # via -r requirements-dev.in -scipy==1.11.4 - # via - # -r requirements-dev.in - # healpy - # scikit-image - # scikit-learn -sentry-sdk==1.36.0 - # via wandb -setproctitle==1.3.3 - # via wandb -six==1.16.0 - # via - # asttokens - # docker-pycreds - # python-dateutil - # tensorboard -smmap==5.0.1 - # via gitdb -stack-data==0.6.3 - # via ipython -sympy==1.12 - # via - # onnxruntime - # torch -tensorboard==2.15.1 - # via -r requirements-dev.in -tensorboard-data-server==0.7.2 - # via tensorboard -tensorrt==8.6.1.post1 - # via -r requirements-dev.in -threadpoolctl==3.2.0 - # via scikit-learn -tifffile==2023.9.26 - # via scikit-image -toml==0.10.2 - # via jupytext -tomli==2.0.1 - # via - # coverage - # pytest -torch==2.1.1 - # via - # -r requirements-dev.in - # lightning - # pytorch-lightning - # torchmetrics - # torchvision -torchmetrics==1.2.0 - # via - # lightning - # pytorch-lightning -torchvision==0.16.1 - # via -r requirements-dev.in -tornado==6.3.3 - # via - # ipykernel - # jupyter-client -tqdm==4.66.1 - # via - # lightning - # pytorch-lightning -traitlets==5.13.0 - # via - # comm - # ipykernel - # ipython - # jupyter-client - # jupyter-core - # matplotlib-inline - # nbformat -triton==2.1.0 - # via torch -typeshed-client==2.4.0 - # via jsonargparse -typing-extensions==4.8.0 - # via - # ipython - # jsonargparse - # lightning - # lightning-utilities - # pytorch-lightning - # torch - # wandb -tzdata==2023.3 - # via pandas -urllib3==2.1.0 - # via - # requests - # sentry-sdk -wandb==0.16.0 - # via -r requirements-dev.in -wcwidth==0.2.11 - # via - # prettytable - # prompt-toolkit -werkzeug==3.0.1 - # via tensorboard -yarl==1.9.3 - # via aiohttp -zipp==3.17.0 - # via - # importlib-metadata - # importlib-resources - -# The following packages are considered to be unsafe in a requirements file: -# setuptools diff --git a/requirements.in b/requirements.in deleted file mode 100644 index 5c2a417..0000000 --- a/requirements.in +++ /dev/null @@ -1,7 +0,0 @@ -astropy==5.3.4 -lightning==2.1.0 -matplotlib==3.7.2 -scikit-image==0.22.0 -scipy==1.11.3 -torch==2.1.0 -torchvision==0.16.0 diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 166d3c8..0000000 --- a/requirements.txt +++ /dev/null @@ -1,191 +0,0 @@ -# -# This file is autogenerated by pip-compile with Python 3.10 -# by the following command: -# -# pip-compile requirements.in -# -aiohttp==3.8.6 - # via fsspec -aiosignal==1.3.1 - # via aiohttp -astropy==5.3.4 - # via -r requirements.in -async-timeout==4.0.3 - # via aiohttp -attrs==23.1.0 - # via aiohttp -certifi==2023.7.22 - # via requests -charset-normalizer==3.3.0 - # via - # aiohttp - # requests -contourpy==1.2.0 - # via matplotlib -cycler==0.12.1 - # via matplotlib -filelock==3.12.4 - # via - # torch - # triton -fonttools==4.44.0 - # via matplotlib -frozenlist==1.4.0 - # via - # aiohttp - # aiosignal -fsspec[http]==2023.9.2 - # via - # lightning - # pytorch-lightning - # torch -idna==3.4 - # via - # requests - # yarl -imageio==2.31.5 - # via scikit-image -jinja2==3.1.2 - # via torch -kiwisolver==1.4.5 - # via matplotlib -lazy-loader==0.3 - # via scikit-image -lightning==2.1.0 - # via -r requirements.in -lightning-utilities==0.9.0 - # via - # lightning - # pytorch-lightning - # torchmetrics -markupsafe==2.1.3 - # via jinja2 -matplotlib==3.7.2 - # via -r requirements.in -mpmath==1.3.0 - # via sympy -multidict==6.0.4 - # via - # aiohttp - # yarl -networkx==3.1 - # via - # scikit-image - # torch -numpy==1.26.0 - # via - # astropy - # contourpy - # imageio - # lightning - # matplotlib - # pyerfa - # pytorch-lightning - # scikit-image - # scipy - # tifffile - # torchmetrics - # torchvision -nvidia-cublas-cu12==12.1.3.1 - # via - # nvidia-cudnn-cu12 - # nvidia-cusolver-cu12 - # torch -nvidia-cuda-cupti-cu12==12.1.105 - # via torch -nvidia-cuda-nvrtc-cu12==12.1.105 - # via torch -nvidia-cuda-runtime-cu12==12.1.105 - # via torch -nvidia-cudnn-cu12==8.9.2.26 - # via torch -nvidia-cufft-cu12==11.0.2.54 - # via torch -nvidia-curand-cu12==10.3.2.106 - # via torch -nvidia-cusolver-cu12==11.4.5.107 - # via torch -nvidia-cusparse-cu12==12.1.0.106 - # via - # nvidia-cusolver-cu12 - # torch -nvidia-nccl-cu12==2.18.1 - # via torch -nvidia-nvjitlink-cu12==12.2.140 - # via - # nvidia-cusolver-cu12 - # nvidia-cusparse-cu12 -nvidia-nvtx-cu12==12.1.105 - # via torch -packaging==23.2 - # via - # astropy - # lightning - # lightning-utilities - # matplotlib - # pytorch-lightning - # scikit-image -pillow==10.0.1 - # via - # imageio - # matplotlib - # scikit-image - # torchvision -pyerfa==2.0.1 - # via astropy -pyparsing==3.0.9 - # via matplotlib -python-dateutil==2.8.2 - # via matplotlib -pytorch-lightning==2.0.9.post0 - # via lightning -pyyaml==6.0.1 - # via - # astropy - # lightning - # pytorch-lightning -requests==2.31.0 - # via - # fsspec - # torchvision -scikit-image==0.22.0 - # via -r requirements.in -scipy==1.11.3 - # via - # -r requirements.in - # scikit-image -six==1.16.0 - # via python-dateutil -sympy==1.12 - # via torch -tifffile==2023.9.26 - # via scikit-image -torch==2.1.0 - # via - # -r requirements.in - # lightning - # pytorch-lightning - # torchmetrics - # torchvision -torchmetrics==1.2.0 - # via - # lightning - # pytorch-lightning -torchvision==0.16.0 - # via -r requirements.in -tqdm==4.66.1 - # via - # lightning - # pytorch-lightning -triton==2.1.0 - # via torch -typing-extensions==4.8.0 - # via - # lightning - # lightning-utilities - # pytorch-lightning - # torch -urllib3==2.0.7 - # via requests -yarl==1.9.2 - # via aiohttp