From fcf3740fc0e13d99c6cf77a1a2d9c04c926f557f Mon Sep 17 00:00:00 2001 From: Hadrien Mary Date: Tue, 6 Jun 2023 14:43:12 -0400 Subject: [PATCH] cleaning pass 2 --- .github/CODEOWNERS | 1 + .github/CODE_OF_CONDUCT.md | 128 ++++++++++++++++++ .github/PULL_REQUEST_TEMPLATE.md | 4 +- .../workflows/{lint.yml => code-check.yml} | 18 +-- .github/workflows/doc.yml | 33 +++-- .github/workflows/release.yml | 112 +++++++++++++++ .github/workflows/test.yml | 22 +-- MANIFEST.in | 8 -- README.md | 70 ++++------ {goli => graphium}/__init__.py | 0 {goli => graphium}/_version.py | 0 {goli => graphium}/cli/README.md | 0 {goli => graphium}/cli/__init__.py | 0 {goli => graphium}/cli/data.py | 0 {goli => graphium}/cli/main.py | 0 {goli => graphium}/config/README.md | 0 {goli => graphium}/config/__init__.py | 0 {goli => graphium}/config/_load.py | 0 {goli => graphium}/config/_loader.py | 0 {goli => graphium}/config/config_convert.py | 0 ..._and_missing_multilevel_multitask_pyg.yaml | 0 .../config/fake_multilevel_multitask_pyg.yaml | 0 .../config/zinc_default_multitask_pyg.yaml | 0 ...atasets_goli-L1000_parse_gctx_to_csv.ipynb | 0 {goli => graphium}/data/QM9/micro_qm9.csv | 0 {goli => graphium}/data/QM9/micro_qm9.parquet | Bin .../data/QM9/norm_micro_qm9.csv | 0 {goli => graphium}/data/QM9/qm9.csv | 0 {goli => graphium}/data/README.md | 0 {goli => graphium}/data/__init__.py | 0 {goli => graphium}/data/collate.py | 0 {goli => graphium}/data/datamodule.py | 0 {goli => graphium}/data/dataset.py | 0 .../make_train_val_test_splits_large.ipynb | 0 .../make_train_val_test_splits_small.ipynb | 0 .../data/micro_ZINC/__init__.py | 0 .../data/micro_ZINC/micro_ZINC.csv | 0 {goli => graphium}/data/multilevel_utils.py | 0 {goli => graphium}/data/multitask/__init__.py | 0 .../data/multitask/tiny_ZINC_SA.csv | 0 .../data/multitask/tiny_ZINC_logp.csv | 0 .../data/multitask/tiny_ZINC_score.csv | 0 {goli => graphium}/data/normalization.py | 0 {goli => graphium}/data/sdf2csv.py | 0 .../single_atom_dataset.csv | 0 {goli => graphium}/data/smiles_transform.py | 0 {goli => graphium}/data/utils.py | 0 .../expts/pyg_batching_sparse.ipynb | 0 {goli => graphium}/features/README.md | 0 {goli => graphium}/features/__init__.py | 0 {goli => graphium}/features/commute.py | 0 {goli => graphium}/features/electrostatic.py | 0 {goli => graphium}/features/featurizer.py | 0 {goli => graphium}/features/graphormer.py | 0 {goli => graphium}/features/nmp.py | 0 .../features/periodic_table.csv | 0 .../features/positional_encoding.py | 0 {goli => graphium}/features/properties.py | 0 {goli => graphium}/features/rw.py | 0 {goli => graphium}/features/spectral.py | 0 .../features/test_new_pes.ipynb | 0 .../features/transfer_pos_level.py | 0 {goli => graphium}/ipu/README.md | 0 {goli => graphium}/ipu/__init__.py | 0 {goli => graphium}/ipu/ipu_dataloader.py | 0 {goli => graphium}/ipu/ipu_losses.py | 0 {goli => graphium}/ipu/ipu_metrics.py | 0 .../ipu/ipu_simple_lightning.py | 0 {goli => graphium}/ipu/ipu_utils.py | 0 {goli => graphium}/ipu/ipu_wrapper.py | 0 {goli => graphium}/ipu/to_dense_batch.py | 0 {goli => graphium}/nn/README.md | 0 {goli => graphium}/nn/__init__.py | 0 {goli => graphium}/nn/architectures/README.md | 0 .../nn/architectures/__init__.py | 0 .../nn/architectures/encoder_manager.py | 0 .../nn/architectures/global_architectures.py | 0 .../nn/architectures/pyg_architectures.py | 0 {goli => graphium}/nn/base_graph_layer.py | 0 {goli => graphium}/nn/base_layers.py | 0 {goli => graphium}/nn/encoders/README.md | 0 {goli => graphium}/nn/encoders/__init__.py | 0 .../nn/encoders/base_encoder.py | 0 .../nn/encoders/bessel_pos_encoder.py | 0 .../encoders/gaussian_kernel_pos_encoder.py | 0 .../nn/encoders/laplace_pos_encoder.py | 0 {goli => graphium}/nn/encoders/mlp_encoder.py | 0 .../nn/encoders/signnet_pos_encoder.py | 0 {goli => graphium}/nn/pyg_layers/README.md | 0 {goli => graphium}/nn/pyg_layers/__init__.py | 0 .../nn/pyg_layers/dimenet_pyg.py | 0 .../nn/pyg_layers/gated_gcn_pyg.py | 0 {goli => graphium}/nn/pyg_layers/gcn_pyg.py | 0 {goli => graphium}/nn/pyg_layers/gin_pyg.py | 0 {goli => graphium}/nn/pyg_layers/gps_pyg.py | 0 {goli => graphium}/nn/pyg_layers/mpnn_pyg.py | 0 {goli => graphium}/nn/pyg_layers/pna_pyg.py | 0 .../nn/pyg_layers/pooling_pyg.py | 0 {goli => graphium}/nn/pyg_layers/utils.py | 0 {goli => graphium}/nn/residual_connections.py | 0 {goli => graphium}/nn/utils.py | 0 {goli => graphium}/trainer/README.md | 0 {goli => graphium}/trainer/__init__.py | 0 {goli => graphium}/trainer/losses.py | 0 {goli => graphium}/trainer/metrics.py | 0 {goli => graphium}/trainer/predictor.py | 0 .../trainer/predictor_options.py | 0 .../trainer/predictor_summaries.py | 0 {goli => graphium}/utils/README.md | 0 {goli => graphium}/utils/__init__.py | 0 {goli => graphium}/utils/arg_checker.py | 0 .../utils/command_line_utils.py | 0 {goli => graphium}/utils/custom_lr.py | 0 {goli => graphium}/utils/decorators.py | 0 {goli => graphium}/utils/dict_tensor.py | 0 {goli => graphium}/utils/fs.py | 0 {goli => graphium}/utils/hashing.py | 0 .../utils/moving_average_tracker.py | 0 {goli => graphium}/utils/mup.py | 0 {goli => graphium}/utils/packing.py | 0 {goli => graphium}/utils/read_file.py | 0 {goli => graphium}/utils/safe_run.py | 0 {goli => graphium}/utils/spaces.py | 0 {goli => graphium}/utils/tensor.py | 0 {goli => graphium}/visualization/README.md | 0 {goli => graphium}/visualization/__init__.py | 0 {goli => graphium}/visualization/vis_utils.py | 0 pyproject.toml | 2 +- 128 files changed, 312 insertions(+), 86 deletions(-) create mode 100644 .github/CODEOWNERS create mode 100644 .github/CODE_OF_CONDUCT.md rename .github/workflows/{lint.yml => code-check.yml} (57%) create mode 100644 .github/workflows/release.yml delete mode 100644 MANIFEST.in rename {goli => graphium}/__init__.py (100%) rename {goli => graphium}/_version.py (100%) rename {goli => graphium}/cli/README.md (100%) rename {goli => graphium}/cli/__init__.py (100%) rename {goli => graphium}/cli/data.py (100%) rename {goli => graphium}/cli/main.py (100%) rename {goli => graphium}/config/README.md (100%) rename {goli => graphium}/config/__init__.py (100%) rename {goli => graphium}/config/_load.py (100%) rename {goli => graphium}/config/_loader.py (100%) rename {goli => graphium}/config/config_convert.py (100%) rename {goli => graphium}/config/fake_and_missing_multilevel_multitask_pyg.yaml (100%) rename {goli => graphium}/config/fake_multilevel_multitask_pyg.yaml (100%) rename {goli => graphium}/config/zinc_default_multitask_pyg.yaml (100%) rename {goli => graphium}/data/L1000/datasets_goli-L1000_parse_gctx_to_csv.ipynb (100%) rename {goli => graphium}/data/QM9/micro_qm9.csv (100%) rename {goli => graphium}/data/QM9/micro_qm9.parquet (100%) rename {goli => graphium}/data/QM9/norm_micro_qm9.csv (100%) rename {goli => graphium}/data/QM9/qm9.csv (100%) rename {goli => graphium}/data/README.md (100%) rename {goli => graphium}/data/__init__.py (100%) rename {goli => graphium}/data/collate.py (100%) rename {goli => graphium}/data/datamodule.py (100%) rename {goli => graphium}/data/dataset.py (100%) rename {goli => graphium}/data/make_data_splits/make_train_val_test_splits_large.ipynb (100%) rename {goli => graphium}/data/make_data_splits/make_train_val_test_splits_small.ipynb (100%) rename {goli => graphium}/data/micro_ZINC/__init__.py (100%) rename {goli => graphium}/data/micro_ZINC/micro_ZINC.csv (100%) rename {goli => graphium}/data/multilevel_utils.py (100%) rename {goli => graphium}/data/multitask/__init__.py (100%) rename {goli => graphium}/data/multitask/tiny_ZINC_SA.csv (100%) rename {goli => graphium}/data/multitask/tiny_ZINC_logp.csv (100%) rename {goli => graphium}/data/multitask/tiny_ZINC_score.csv (100%) rename {goli => graphium}/data/normalization.py (100%) rename {goli => graphium}/data/sdf2csv.py (100%) rename {goli => graphium}/data/single_atom_dataset/single_atom_dataset.csv (100%) rename {goli => graphium}/data/smiles_transform.py (100%) rename {goli => graphium}/data/utils.py (100%) rename {goli => graphium}/expts/pyg_batching_sparse.ipynb (100%) rename {goli => graphium}/features/README.md (100%) rename {goli => graphium}/features/__init__.py (100%) rename {goli => graphium}/features/commute.py (100%) rename {goli => graphium}/features/electrostatic.py (100%) rename {goli => graphium}/features/featurizer.py (100%) rename {goli => graphium}/features/graphormer.py (100%) rename {goli => graphium}/features/nmp.py (100%) rename {goli => graphium}/features/periodic_table.csv (100%) rename {goli => graphium}/features/positional_encoding.py (100%) rename {goli => graphium}/features/properties.py (100%) rename {goli => graphium}/features/rw.py (100%) rename {goli => graphium}/features/spectral.py (100%) rename {goli => graphium}/features/test_new_pes.ipynb (100%) rename {goli => graphium}/features/transfer_pos_level.py (100%) rename {goli => graphium}/ipu/README.md (100%) rename {goli => graphium}/ipu/__init__.py (100%) rename {goli => graphium}/ipu/ipu_dataloader.py (100%) rename {goli => graphium}/ipu/ipu_losses.py (100%) rename {goli => graphium}/ipu/ipu_metrics.py (100%) rename {goli => graphium}/ipu/ipu_simple_lightning.py (100%) rename {goli => graphium}/ipu/ipu_utils.py (100%) rename {goli => graphium}/ipu/ipu_wrapper.py (100%) rename {goli => graphium}/ipu/to_dense_batch.py (100%) rename {goli => graphium}/nn/README.md (100%) rename {goli => graphium}/nn/__init__.py (100%) rename {goli => graphium}/nn/architectures/README.md (100%) rename {goli => graphium}/nn/architectures/__init__.py (100%) rename {goli => graphium}/nn/architectures/encoder_manager.py (100%) rename {goli => graphium}/nn/architectures/global_architectures.py (100%) rename {goli => graphium}/nn/architectures/pyg_architectures.py (100%) rename {goli => graphium}/nn/base_graph_layer.py (100%) rename {goli => graphium}/nn/base_layers.py (100%) rename {goli => graphium}/nn/encoders/README.md (100%) rename {goli => graphium}/nn/encoders/__init__.py (100%) rename {goli => graphium}/nn/encoders/base_encoder.py (100%) rename {goli => graphium}/nn/encoders/bessel_pos_encoder.py (100%) rename {goli => graphium}/nn/encoders/gaussian_kernel_pos_encoder.py (100%) rename {goli => graphium}/nn/encoders/laplace_pos_encoder.py (100%) rename {goli => graphium}/nn/encoders/mlp_encoder.py (100%) rename {goli => graphium}/nn/encoders/signnet_pos_encoder.py (100%) rename {goli => graphium}/nn/pyg_layers/README.md (100%) rename {goli => graphium}/nn/pyg_layers/__init__.py (100%) rename {goli => graphium}/nn/pyg_layers/dimenet_pyg.py (100%) rename {goli => graphium}/nn/pyg_layers/gated_gcn_pyg.py (100%) rename {goli => graphium}/nn/pyg_layers/gcn_pyg.py (100%) rename {goli => graphium}/nn/pyg_layers/gin_pyg.py (100%) rename {goli => graphium}/nn/pyg_layers/gps_pyg.py (100%) rename {goli => graphium}/nn/pyg_layers/mpnn_pyg.py (100%) rename {goli => graphium}/nn/pyg_layers/pna_pyg.py (100%) rename {goli => graphium}/nn/pyg_layers/pooling_pyg.py (100%) rename {goli => graphium}/nn/pyg_layers/utils.py (100%) rename {goli => graphium}/nn/residual_connections.py (100%) rename {goli => graphium}/nn/utils.py (100%) rename {goli => graphium}/trainer/README.md (100%) rename {goli => graphium}/trainer/__init__.py (100%) rename {goli => graphium}/trainer/losses.py (100%) rename {goli => graphium}/trainer/metrics.py (100%) rename {goli => graphium}/trainer/predictor.py (100%) rename {goli => graphium}/trainer/predictor_options.py (100%) rename {goli => graphium}/trainer/predictor_summaries.py (100%) rename {goli => graphium}/utils/README.md (100%) rename {goli => graphium}/utils/__init__.py (100%) rename {goli => graphium}/utils/arg_checker.py (100%) rename {goli => graphium}/utils/command_line_utils.py (100%) rename {goli => graphium}/utils/custom_lr.py (100%) rename {goli => graphium}/utils/decorators.py (100%) rename {goli => graphium}/utils/dict_tensor.py (100%) rename {goli => graphium}/utils/fs.py (100%) rename {goli => graphium}/utils/hashing.py (100%) rename {goli => graphium}/utils/moving_average_tracker.py (100%) rename {goli => graphium}/utils/mup.py (100%) rename {goli => graphium}/utils/packing.py (100%) rename {goli => graphium}/utils/read_file.py (100%) rename {goli => graphium}/utils/safe_run.py (100%) rename {goli => graphium}/utils/spaces.py (100%) rename {goli => graphium}/utils/tensor.py (100%) rename {goli => graphium}/visualization/README.md (100%) rename {goli => graphium}/visualization/__init__.py (100%) rename {goli => graphium}/visualization/vis_utils.py (100%) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS new file mode 100644 index 000000000..98cac96b2 --- /dev/null +++ b/.github/CODEOWNERS @@ -0,0 +1 @@ +* @DomInvivo diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md new file mode 100644 index 000000000..18c914718 --- /dev/null +++ b/.github/CODE_OF_CONDUCT.md @@ -0,0 +1,128 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socio-economic status, +nationality, personal appearance, race, religion, or sexual identity +and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +* Demonstrating empathy and kindness toward other people +* Being respectful of differing opinions, viewpoints, and experiences +* Giving and gracefully accepting constructive feedback +* Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +* Focusing on what is best not just for us as individuals, but for the + overall community + +Examples of unacceptable behavior include: + +* The use of sexualized language or imagery, and sexual attention or + advances of any kind +* Trolling, insulting or derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or email + address, without their explicit permission +* Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official e-mail address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to the community leaders responsible for enforcement at +. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series +of actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or +permanent ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within +the community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.0, available at +https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. + +Community Impact Guidelines were inspired by [Mozilla's code of conduct +enforcement ladder](https://github.com/mozilla/diversity). + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see the FAQ at +https://www.contributor-covenant.org/faq. Translations are available at +https://www.contributor-covenant.org/translations. diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 56db38d4a..ee1bbedcf 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,5 +1,7 @@ Checklist: -- [ ] Added a `news` entry: _copy `news/TEMPLATE.rst` to `news/my-feature-or-branch.rst`) and edit it._ +- [ ] Was this PR discussed in a issue? It is recommended to first discuss a new feature into a GitHub issue before opening a PR. +- [ ] Add tests to cover the fixed bug(s) or the new introduced feature(s) (if appropriate). +- [ ] Update the API documentation is a new function is added or an existing one is deleted. --- diff --git a/.github/workflows/lint.yml b/.github/workflows/code-check.yml similarity index 57% rename from .github/workflows/lint.yml rename to .github/workflows/code-check.yml index ddaf40412..d5a28b611 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/code-check.yml @@ -1,26 +1,26 @@ -name: Lint +name: code-check on: push: - branches: - - "master" + branches: ["main"] + tags: ["*"] pull_request: branches: - "*" + - "!gh-pages" jobs: - lint-source-code: - name: Lint - runs-on: "ubuntu-latest" - + python-format-black: + name: Python lint [black] + runs-on: ubuntu-latest steps: - name: Checkout the code uses: actions/checkout@v3 - name: Set up Python - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: - python-version: 3.9 + python-version: "3.10" - name: Install black run: | diff --git a/.github/workflows/doc.yml b/.github/workflows/doc.yml index 27bb74f04..cc9017762 100644 --- a/.github/workflows/doc.yml +++ b/.github/workflows/doc.yml @@ -2,8 +2,9 @@ name: doc on: push: - branches: - - "master" + branches: ["main"] + release: + types: [published] jobs: doc: @@ -18,22 +19,34 @@ jobs: - name: Checkout the code uses: actions/checkout@v3 - - name: Setup Mamba - uses: mamba-org/provision-with-micromamba@v14 + - name: Setup mamba + uses: mamba-org/setup-micromamba@v1 with: environment-file: env.yml - environment-name: goli + environment-name: openfractal + cache-environment: true cache-downloads: true - cache-env: true - channel-priority: strict - name: Install library run: python -m pip install --no-deps . - name: Deploy the doc run: | - # Get the privpage branch + echo "Configure git" + git config --global user.name "${GITHUB_ACTOR}" + git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com" + + echo "Get the gh-pages branch" git fetch origin gh-pages - # Build and serve the doc - mkdocs gh-deploy --force + TAG_OR_BRANCH_NAME=${GITHUB_REF##*/} + + if [ $TAG_OR_BRANCH_NAME = "main" ]; then + echo "Build and deploy the doc on main" + mike deploy --push --force main + else + echo "Build and deploy the doc on $TAG_OR_BRANCH_NAME" + + mike deploy --push --force stable + mike deploy --push --force $TAG_OR_BRANCH_NAME + fi diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 000000000..cb8949f16 --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,112 @@ +name: release + +on: + workflow_dispatch: + inputs: + release-version: + description: "A valid Semver version string" + required: true + +permissions: + contents: write + pull-requests: write + +jobs: + release: + # Do not release if not triggered from the default branch + if: github.ref == format('refs/heads/{0}', github.event.repository.default_branch) + + runs-on: ubuntu-latest + timeout-minutes: 30 + + defaults: + run: + shell: bash -l {0} + + steps: + - name: Checkout the code + uses: actions/checkout@v3 + + - name: Setup mamba + uses: mamba-org/setup-micromamba@v1 + with: + environment-file: env.yml + environment-name: graphium + cache-environment: true + cache-downloads: true + create-args: >- + pip + semver + python-build + setuptools_scm + + - name: Check the version is valid semver + run: | + RELEASE_VERSION="${{ inputs.release-version }}" + + { + pysemver check $RELEASE_VERSION + } || { + echo "The version '$RELEASE_VERSION' is not a valid Semver version string." + echo "Please use a valid semver version string. More details at https://semver.org/" + echo "The release process is aborted." + exit 1 + } + + - name: Check the version is higher than the latest one + run: | + # Retrieve the git tags first + git fetch --prune --unshallow --tags &> /dev/null + + RELEASE_VERSION="${{ inputs.release-version }}" + LATEST_VERSION=$(git describe --abbrev=0 --tags) + + IS_HIGHER_VERSION=$(pysemver compare $RELEASE_VERSION $LATEST_VERSION) + + if [ "$IS_HIGHER_VERSION" != "1" ]; then + echo "The version '$RELEASE_VERSION' is not higher than the latest version '$LATEST_VERSION'." + echo "The release process is aborted." + exit 1 + fi + + - name: Build Changelog + id: github_release + uses: mikepenz/release-changelog-builder-action@v4 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + + - name: Configure git + run: | + git config --global user.name "${GITHUB_ACTOR}" + git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com" + + - name: Create and push git tag + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: | + # Tag the release + git tag -a "${{ inputs.release-version }}" -m "Release version ${{ inputs.release-version }}" + + # Push the modified changelogs + git push origin main + + # Push the tags + git push origin "${{ inputs.release-version }}" + + - name: Install library + run: python -m pip install --no-deps . + + - name: Build the wheel and sdist + run: python -m build --no-isolation + + - name: Publish package to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 + with: + password: ${{ secrets.PYPI_API_TOKEN }} + packages-dir: dist/ + + - name: Create GitHub Release + uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844 + with: + tag_name: ${{ inputs.release-version }} + body: ${{steps.github_release.outputs.changelog}} diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 920fdb375..434661963 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -2,11 +2,14 @@ name: test on: push: - branches: - - "master" + branches: ["main"] + tags: ["*"] pull_request: branches: - "*" + - "!gh-pages" + schedule: + - cron: "0 4 * * MON" jobs: test: @@ -31,17 +34,16 @@ jobs: - name: Checkout the code uses: actions/checkout@v3 - - name: Setup Mamba - uses: mamba-org/provision-with-micromamba@v15 + - name: Setup mamba + uses: mamba-org/setup-micromamba@v1 with: environment-file: env.yml - environment-name: goli - extra-specs: | + environment-name: graphium + cache-environment: true + cache-downloads: true + create-args: >- python=${{ matrix.python-version }} pytorch=${{ matrix.pytorch-version }} - cache-downloads: true - cache-env: true - channel-priority: strict - name: Install library run: python -m pip install --no-deps . @@ -50,7 +52,7 @@ jobs: run: pytest - name: Test CLI - run: goli --help + run: graphium --help - name: Test building the doc run: mkdocs build diff --git a/MANIFEST.in b/MANIFEST.in deleted file mode 100644 index 36d7eed6d..000000000 --- a/MANIFEST.in +++ /dev/null @@ -1,8 +0,0 @@ -include README.md -include *.py -graft goli/*.yaml -recursive-include goli/ *.csv -recursive-include goli/config/ *.yaml -recursive-exclude * __pycache__ -recursive-exclude * *.py[co] -recursive-exclude * .ipynb_checkpoints/* diff --git a/README.md b/README.md index f32cefae2..16103d454 100644 --- a/README.md +++ b/README.md @@ -1,19 +1,14 @@
-

The Graph Of LIfe Library.

+

Scaling molecular GNNs to infinity.

--- -[![Binder](http://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/valence-discovery/goli/master?urlpath=lab/tree/docs/tutorials/) -[![PyPI](https://img.shields.io/pypi/v/goli)](https://pypi.org/project/goli-life/) -[![Conda](https://img.shields.io/conda/v/conda-forge/goli?label=conda&color=success)](https://anaconda.org/conda-forge/goli) -[![PyPI - Downloads](https://img.shields.io/pypi/dm/goli-life)](https://pypi.org/project/goli/) -[![Conda](https://img.shields.io/conda/dn/conda-forge/goli)](https://anaconda.org/conda-forge/goli) -[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/goli-life)](https://pypi.org/project/goli-life/) -[![license](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/valence-discovery/goli/blob/master/LICENSE) -[![GitHub Repo stars](https://img.shields.io/github/stars/valence-discovery/goli)](https://github.com/valence-discovery/goli/stargazers) -[![GitHub Repo stars](https://img.shields.io/github/forks/valence-discovery/goli)](https://github.com/valence-discovery/goli/network/members) +[![test](https://github.com/datamol-io/graphium/actions/workflows/test.yml/badge.svg)](https://github.com/datamol-io/graphium/actions/workflows/test.yml) +[![release](https://github.com/datamol-io/graphium/actions/workflows/release.yml/badge.svg)](https://github.com/datamol-io/graphium/actions/workflows/release.yml) +[![code-check](https://github.com/datamol-io/graphium/actions/workflows/code-check.yml/badge.svg)](https://github.com/datamol-io/graphium/actions/workflows/code-check.yml) +[![doc](https://github.com/datamol-io/graphium/actions/workflows/doc.yml/badge.svg)](https://github.com/datamol-io/graphium/actions/workflows/doc.yml) A deep learning library focused on graph representation learning for real-world chemical tasks. @@ -24,38 +19,31 @@ A deep learning library focused on graph representation learning for real-world - ⮔ Read-to-use training loop based on [Pytorch Lightning](https://www.pytorchlightning.ai/). - 🔌 Have a new dataset? Goli provides a simple plug-and-play interface. Change the path, the name of the columns to predict, the atomic featurization, and you’re ready to play! -## Try Online - -Visit [![Binder](http://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/valence-discovery/goli/master?urlpath=lab/tree/docs/tutorials/) and try Goli online. - ## Documentation -Visit https://valence-discovery.github.io/goli/. +Visit https://graphium-docs.datamol.io/. ## Installation for developers -### For CPU and GPU developers installs +### For CPU and GPU developers -Use either [`mamba`](https://github.com/mamba-org/mamba) or [`conda`](https://docs.conda.io/en/latest/): +Use [`mamba`](https://github.com/mamba-org/mamba): ```bash -# Install mamba if unavailable -conda install -c conda-forge mamba - -# Install Goli's dependencies in a new environment named `goli_dev` -mamba env create -f env.yml -n goli_dev +# Install Graphium's dependencies in a new environment named `graphium` +mamba env create -f env.yml -n graphium -# Install Goli in dev mode -conda activate goli_dev +# Install Graphium in dev mode +conda activate graphium pip install -e . ``` -### For IPU developers installs +### For IPU developers ```bash -mkdir ~/.venv # Create the folder for the environment -python3 -m venv ~/.venv/goli_ipu # Create the environment -source ~/.venv/goli_ipu/bin/activate # Activate the environment +mkdir ~/.venv # Create the folder for the environment +python3 -m venv ~/.venv/graphium_ipu # Create the environment +source ~/.venv/graphium_ipu/bin/activate # Activate the environment # Installing the poptorch SDK. Make sure to change the path pip install PATH_TO_SDK/poptorch-3.2.0+109946_bb50ce43ab_ubuntu_20_04-cp38-cp38-linux_x86_64.whl @@ -63,41 +51,29 @@ pip install PATH_TO_SDK/poptorch-3.2.0+109946_bb50ce43ab_ubuntu_20_04-cp38-cp38- # Activate poplar SDK. source PATH_TO_SDK/enable -# Install the IPU specific and goli requirements +# Install the IPU specific and graphium requirements PACKAGE_NAME=pytorch pip install -r requirements_ipu.txt -# Install Goli in dev mode +# Install Graphium in dev mode pip install -e . ``` ## Training a model -To learn how to train a model, we invite you to look at the documentation, or the jupyter notebooks available [here](https://github.com/valence-discovery/goli/tree/master/docs/tutorials/model_training). +To learn how to train a model, we invite you to look at the documentation, or the jupyter notebooks available [here](https://github.com/datamol-io/graphium/tree/master/docs/tutorials/model_training). If you are not familiar with [PyTorch](https://pytorch.org/docs) or [PyTorch-Lightning](https://pytorch-lightning.readthedocs.io/en/latest/), we highly recommend going through their tutorial first. -## Changelogs - -See the latest changelogs at [CHANGELOG.rst](./CHANGELOG.rst). - ## License Under the Apache-2.0 license. See [LICENSE](LICENSE). -## Authors - -See [AUTHORS.rst](./AUTHORS.rst). - ## Documentation -* Diagram for data processing in molGPS. - -Data Processing Chart - - - -* Diagram for Muti-task network in molGPS +- Diagram for data processing in molGPS. -Full Graph Multi-task Network +Data Processing Chart +- Diagram for Muti-task network in molGPS +Full Graph Multi-task Network diff --git a/goli/__init__.py b/graphium/__init__.py similarity index 100% rename from goli/__init__.py rename to graphium/__init__.py diff --git a/goli/_version.py b/graphium/_version.py similarity index 100% rename from goli/_version.py rename to graphium/_version.py diff --git a/goli/cli/README.md b/graphium/cli/README.md similarity index 100% rename from goli/cli/README.md rename to graphium/cli/README.md diff --git a/goli/cli/__init__.py b/graphium/cli/__init__.py similarity index 100% rename from goli/cli/__init__.py rename to graphium/cli/__init__.py diff --git a/goli/cli/data.py b/graphium/cli/data.py similarity index 100% rename from goli/cli/data.py rename to graphium/cli/data.py diff --git a/goli/cli/main.py b/graphium/cli/main.py similarity index 100% rename from goli/cli/main.py rename to graphium/cli/main.py diff --git a/goli/config/README.md b/graphium/config/README.md similarity index 100% rename from goli/config/README.md rename to graphium/config/README.md diff --git a/goli/config/__init__.py b/graphium/config/__init__.py similarity index 100% rename from goli/config/__init__.py rename to graphium/config/__init__.py diff --git a/goli/config/_load.py b/graphium/config/_load.py similarity index 100% rename from goli/config/_load.py rename to graphium/config/_load.py diff --git a/goli/config/_loader.py b/graphium/config/_loader.py similarity index 100% rename from goli/config/_loader.py rename to graphium/config/_loader.py diff --git a/goli/config/config_convert.py b/graphium/config/config_convert.py similarity index 100% rename from goli/config/config_convert.py rename to graphium/config/config_convert.py diff --git a/goli/config/fake_and_missing_multilevel_multitask_pyg.yaml b/graphium/config/fake_and_missing_multilevel_multitask_pyg.yaml similarity index 100% rename from goli/config/fake_and_missing_multilevel_multitask_pyg.yaml rename to graphium/config/fake_and_missing_multilevel_multitask_pyg.yaml diff --git a/goli/config/fake_multilevel_multitask_pyg.yaml b/graphium/config/fake_multilevel_multitask_pyg.yaml similarity index 100% rename from goli/config/fake_multilevel_multitask_pyg.yaml rename to graphium/config/fake_multilevel_multitask_pyg.yaml diff --git a/goli/config/zinc_default_multitask_pyg.yaml b/graphium/config/zinc_default_multitask_pyg.yaml similarity index 100% rename from goli/config/zinc_default_multitask_pyg.yaml rename to graphium/config/zinc_default_multitask_pyg.yaml diff --git a/goli/data/L1000/datasets_goli-L1000_parse_gctx_to_csv.ipynb b/graphium/data/L1000/datasets_goli-L1000_parse_gctx_to_csv.ipynb similarity index 100% rename from goli/data/L1000/datasets_goli-L1000_parse_gctx_to_csv.ipynb rename to graphium/data/L1000/datasets_goli-L1000_parse_gctx_to_csv.ipynb diff --git a/goli/data/QM9/micro_qm9.csv b/graphium/data/QM9/micro_qm9.csv similarity index 100% rename from goli/data/QM9/micro_qm9.csv rename to graphium/data/QM9/micro_qm9.csv diff --git a/goli/data/QM9/micro_qm9.parquet b/graphium/data/QM9/micro_qm9.parquet similarity index 100% rename from goli/data/QM9/micro_qm9.parquet rename to graphium/data/QM9/micro_qm9.parquet diff --git a/goli/data/QM9/norm_micro_qm9.csv b/graphium/data/QM9/norm_micro_qm9.csv similarity index 100% rename from goli/data/QM9/norm_micro_qm9.csv rename to graphium/data/QM9/norm_micro_qm9.csv diff --git a/goli/data/QM9/qm9.csv b/graphium/data/QM9/qm9.csv similarity index 100% rename from goli/data/QM9/qm9.csv rename to graphium/data/QM9/qm9.csv diff --git a/goli/data/README.md b/graphium/data/README.md similarity index 100% rename from goli/data/README.md rename to graphium/data/README.md diff --git a/goli/data/__init__.py b/graphium/data/__init__.py similarity index 100% rename from goli/data/__init__.py rename to graphium/data/__init__.py diff --git a/goli/data/collate.py b/graphium/data/collate.py similarity index 100% rename from goli/data/collate.py rename to graphium/data/collate.py diff --git a/goli/data/datamodule.py b/graphium/data/datamodule.py similarity index 100% rename from goli/data/datamodule.py rename to graphium/data/datamodule.py diff --git a/goli/data/dataset.py b/graphium/data/dataset.py similarity index 100% rename from goli/data/dataset.py rename to graphium/data/dataset.py diff --git a/goli/data/make_data_splits/make_train_val_test_splits_large.ipynb b/graphium/data/make_data_splits/make_train_val_test_splits_large.ipynb similarity index 100% rename from goli/data/make_data_splits/make_train_val_test_splits_large.ipynb rename to graphium/data/make_data_splits/make_train_val_test_splits_large.ipynb diff --git a/goli/data/make_data_splits/make_train_val_test_splits_small.ipynb b/graphium/data/make_data_splits/make_train_val_test_splits_small.ipynb similarity index 100% rename from goli/data/make_data_splits/make_train_val_test_splits_small.ipynb rename to graphium/data/make_data_splits/make_train_val_test_splits_small.ipynb diff --git a/goli/data/micro_ZINC/__init__.py b/graphium/data/micro_ZINC/__init__.py similarity index 100% rename from goli/data/micro_ZINC/__init__.py rename to graphium/data/micro_ZINC/__init__.py diff --git a/goli/data/micro_ZINC/micro_ZINC.csv b/graphium/data/micro_ZINC/micro_ZINC.csv similarity index 100% rename from goli/data/micro_ZINC/micro_ZINC.csv rename to graphium/data/micro_ZINC/micro_ZINC.csv diff --git a/goli/data/multilevel_utils.py b/graphium/data/multilevel_utils.py similarity index 100% rename from goli/data/multilevel_utils.py rename to graphium/data/multilevel_utils.py diff --git a/goli/data/multitask/__init__.py b/graphium/data/multitask/__init__.py similarity index 100% rename from goli/data/multitask/__init__.py rename to graphium/data/multitask/__init__.py diff --git a/goli/data/multitask/tiny_ZINC_SA.csv b/graphium/data/multitask/tiny_ZINC_SA.csv similarity index 100% rename from goli/data/multitask/tiny_ZINC_SA.csv rename to graphium/data/multitask/tiny_ZINC_SA.csv diff --git a/goli/data/multitask/tiny_ZINC_logp.csv b/graphium/data/multitask/tiny_ZINC_logp.csv similarity index 100% rename from goli/data/multitask/tiny_ZINC_logp.csv rename to graphium/data/multitask/tiny_ZINC_logp.csv diff --git a/goli/data/multitask/tiny_ZINC_score.csv b/graphium/data/multitask/tiny_ZINC_score.csv similarity index 100% rename from goli/data/multitask/tiny_ZINC_score.csv rename to graphium/data/multitask/tiny_ZINC_score.csv diff --git a/goli/data/normalization.py b/graphium/data/normalization.py similarity index 100% rename from goli/data/normalization.py rename to graphium/data/normalization.py diff --git a/goli/data/sdf2csv.py b/graphium/data/sdf2csv.py similarity index 100% rename from goli/data/sdf2csv.py rename to graphium/data/sdf2csv.py diff --git a/goli/data/single_atom_dataset/single_atom_dataset.csv b/graphium/data/single_atom_dataset/single_atom_dataset.csv similarity index 100% rename from goli/data/single_atom_dataset/single_atom_dataset.csv rename to graphium/data/single_atom_dataset/single_atom_dataset.csv diff --git a/goli/data/smiles_transform.py b/graphium/data/smiles_transform.py similarity index 100% rename from goli/data/smiles_transform.py rename to graphium/data/smiles_transform.py diff --git a/goli/data/utils.py b/graphium/data/utils.py similarity index 100% rename from goli/data/utils.py rename to graphium/data/utils.py diff --git a/goli/expts/pyg_batching_sparse.ipynb b/graphium/expts/pyg_batching_sparse.ipynb similarity index 100% rename from goli/expts/pyg_batching_sparse.ipynb rename to graphium/expts/pyg_batching_sparse.ipynb diff --git a/goli/features/README.md b/graphium/features/README.md similarity index 100% rename from goli/features/README.md rename to graphium/features/README.md diff --git a/goli/features/__init__.py b/graphium/features/__init__.py similarity index 100% rename from goli/features/__init__.py rename to graphium/features/__init__.py diff --git a/goli/features/commute.py b/graphium/features/commute.py similarity index 100% rename from goli/features/commute.py rename to graphium/features/commute.py diff --git a/goli/features/electrostatic.py b/graphium/features/electrostatic.py similarity index 100% rename from goli/features/electrostatic.py rename to graphium/features/electrostatic.py diff --git a/goli/features/featurizer.py b/graphium/features/featurizer.py similarity index 100% rename from goli/features/featurizer.py rename to graphium/features/featurizer.py diff --git a/goli/features/graphormer.py b/graphium/features/graphormer.py similarity index 100% rename from goli/features/graphormer.py rename to graphium/features/graphormer.py diff --git a/goli/features/nmp.py b/graphium/features/nmp.py similarity index 100% rename from goli/features/nmp.py rename to graphium/features/nmp.py diff --git a/goli/features/periodic_table.csv b/graphium/features/periodic_table.csv similarity index 100% rename from goli/features/periodic_table.csv rename to graphium/features/periodic_table.csv diff --git a/goli/features/positional_encoding.py b/graphium/features/positional_encoding.py similarity index 100% rename from goli/features/positional_encoding.py rename to graphium/features/positional_encoding.py diff --git a/goli/features/properties.py b/graphium/features/properties.py similarity index 100% rename from goli/features/properties.py rename to graphium/features/properties.py diff --git a/goli/features/rw.py b/graphium/features/rw.py similarity index 100% rename from goli/features/rw.py rename to graphium/features/rw.py diff --git a/goli/features/spectral.py b/graphium/features/spectral.py similarity index 100% rename from goli/features/spectral.py rename to graphium/features/spectral.py diff --git a/goli/features/test_new_pes.ipynb b/graphium/features/test_new_pes.ipynb similarity index 100% rename from goli/features/test_new_pes.ipynb rename to graphium/features/test_new_pes.ipynb diff --git a/goli/features/transfer_pos_level.py b/graphium/features/transfer_pos_level.py similarity index 100% rename from goli/features/transfer_pos_level.py rename to graphium/features/transfer_pos_level.py diff --git a/goli/ipu/README.md b/graphium/ipu/README.md similarity index 100% rename from goli/ipu/README.md rename to graphium/ipu/README.md diff --git a/goli/ipu/__init__.py b/graphium/ipu/__init__.py similarity index 100% rename from goli/ipu/__init__.py rename to graphium/ipu/__init__.py diff --git a/goli/ipu/ipu_dataloader.py b/graphium/ipu/ipu_dataloader.py similarity index 100% rename from goli/ipu/ipu_dataloader.py rename to graphium/ipu/ipu_dataloader.py diff --git a/goli/ipu/ipu_losses.py b/graphium/ipu/ipu_losses.py similarity index 100% rename from goli/ipu/ipu_losses.py rename to graphium/ipu/ipu_losses.py diff --git a/goli/ipu/ipu_metrics.py b/graphium/ipu/ipu_metrics.py similarity index 100% rename from goli/ipu/ipu_metrics.py rename to graphium/ipu/ipu_metrics.py diff --git a/goli/ipu/ipu_simple_lightning.py b/graphium/ipu/ipu_simple_lightning.py similarity index 100% rename from goli/ipu/ipu_simple_lightning.py rename to graphium/ipu/ipu_simple_lightning.py diff --git a/goli/ipu/ipu_utils.py b/graphium/ipu/ipu_utils.py similarity index 100% rename from goli/ipu/ipu_utils.py rename to graphium/ipu/ipu_utils.py diff --git a/goli/ipu/ipu_wrapper.py b/graphium/ipu/ipu_wrapper.py similarity index 100% rename from goli/ipu/ipu_wrapper.py rename to graphium/ipu/ipu_wrapper.py diff --git a/goli/ipu/to_dense_batch.py b/graphium/ipu/to_dense_batch.py similarity index 100% rename from goli/ipu/to_dense_batch.py rename to graphium/ipu/to_dense_batch.py diff --git a/goli/nn/README.md b/graphium/nn/README.md similarity index 100% rename from goli/nn/README.md rename to graphium/nn/README.md diff --git a/goli/nn/__init__.py b/graphium/nn/__init__.py similarity index 100% rename from goli/nn/__init__.py rename to graphium/nn/__init__.py diff --git a/goli/nn/architectures/README.md b/graphium/nn/architectures/README.md similarity index 100% rename from goli/nn/architectures/README.md rename to graphium/nn/architectures/README.md diff --git a/goli/nn/architectures/__init__.py b/graphium/nn/architectures/__init__.py similarity index 100% rename from goli/nn/architectures/__init__.py rename to graphium/nn/architectures/__init__.py diff --git a/goli/nn/architectures/encoder_manager.py b/graphium/nn/architectures/encoder_manager.py similarity index 100% rename from goli/nn/architectures/encoder_manager.py rename to graphium/nn/architectures/encoder_manager.py diff --git a/goli/nn/architectures/global_architectures.py b/graphium/nn/architectures/global_architectures.py similarity index 100% rename from goli/nn/architectures/global_architectures.py rename to graphium/nn/architectures/global_architectures.py diff --git a/goli/nn/architectures/pyg_architectures.py b/graphium/nn/architectures/pyg_architectures.py similarity index 100% rename from goli/nn/architectures/pyg_architectures.py rename to graphium/nn/architectures/pyg_architectures.py diff --git a/goli/nn/base_graph_layer.py b/graphium/nn/base_graph_layer.py similarity index 100% rename from goli/nn/base_graph_layer.py rename to graphium/nn/base_graph_layer.py diff --git a/goli/nn/base_layers.py b/graphium/nn/base_layers.py similarity index 100% rename from goli/nn/base_layers.py rename to graphium/nn/base_layers.py diff --git a/goli/nn/encoders/README.md b/graphium/nn/encoders/README.md similarity index 100% rename from goli/nn/encoders/README.md rename to graphium/nn/encoders/README.md diff --git a/goli/nn/encoders/__init__.py b/graphium/nn/encoders/__init__.py similarity index 100% rename from goli/nn/encoders/__init__.py rename to graphium/nn/encoders/__init__.py diff --git a/goli/nn/encoders/base_encoder.py b/graphium/nn/encoders/base_encoder.py similarity index 100% rename from goli/nn/encoders/base_encoder.py rename to graphium/nn/encoders/base_encoder.py diff --git a/goli/nn/encoders/bessel_pos_encoder.py b/graphium/nn/encoders/bessel_pos_encoder.py similarity index 100% rename from goli/nn/encoders/bessel_pos_encoder.py rename to graphium/nn/encoders/bessel_pos_encoder.py diff --git a/goli/nn/encoders/gaussian_kernel_pos_encoder.py b/graphium/nn/encoders/gaussian_kernel_pos_encoder.py similarity index 100% rename from goli/nn/encoders/gaussian_kernel_pos_encoder.py rename to graphium/nn/encoders/gaussian_kernel_pos_encoder.py diff --git a/goli/nn/encoders/laplace_pos_encoder.py b/graphium/nn/encoders/laplace_pos_encoder.py similarity index 100% rename from goli/nn/encoders/laplace_pos_encoder.py rename to graphium/nn/encoders/laplace_pos_encoder.py diff --git a/goli/nn/encoders/mlp_encoder.py b/graphium/nn/encoders/mlp_encoder.py similarity index 100% rename from goli/nn/encoders/mlp_encoder.py rename to graphium/nn/encoders/mlp_encoder.py diff --git a/goli/nn/encoders/signnet_pos_encoder.py b/graphium/nn/encoders/signnet_pos_encoder.py similarity index 100% rename from goli/nn/encoders/signnet_pos_encoder.py rename to graphium/nn/encoders/signnet_pos_encoder.py diff --git a/goli/nn/pyg_layers/README.md b/graphium/nn/pyg_layers/README.md similarity index 100% rename from goli/nn/pyg_layers/README.md rename to graphium/nn/pyg_layers/README.md diff --git a/goli/nn/pyg_layers/__init__.py b/graphium/nn/pyg_layers/__init__.py similarity index 100% rename from goli/nn/pyg_layers/__init__.py rename to graphium/nn/pyg_layers/__init__.py diff --git a/goli/nn/pyg_layers/dimenet_pyg.py b/graphium/nn/pyg_layers/dimenet_pyg.py similarity index 100% rename from goli/nn/pyg_layers/dimenet_pyg.py rename to graphium/nn/pyg_layers/dimenet_pyg.py diff --git a/goli/nn/pyg_layers/gated_gcn_pyg.py b/graphium/nn/pyg_layers/gated_gcn_pyg.py similarity index 100% rename from goli/nn/pyg_layers/gated_gcn_pyg.py rename to graphium/nn/pyg_layers/gated_gcn_pyg.py diff --git a/goli/nn/pyg_layers/gcn_pyg.py b/graphium/nn/pyg_layers/gcn_pyg.py similarity index 100% rename from goli/nn/pyg_layers/gcn_pyg.py rename to graphium/nn/pyg_layers/gcn_pyg.py diff --git a/goli/nn/pyg_layers/gin_pyg.py b/graphium/nn/pyg_layers/gin_pyg.py similarity index 100% rename from goli/nn/pyg_layers/gin_pyg.py rename to graphium/nn/pyg_layers/gin_pyg.py diff --git a/goli/nn/pyg_layers/gps_pyg.py b/graphium/nn/pyg_layers/gps_pyg.py similarity index 100% rename from goli/nn/pyg_layers/gps_pyg.py rename to graphium/nn/pyg_layers/gps_pyg.py diff --git a/goli/nn/pyg_layers/mpnn_pyg.py b/graphium/nn/pyg_layers/mpnn_pyg.py similarity index 100% rename from goli/nn/pyg_layers/mpnn_pyg.py rename to graphium/nn/pyg_layers/mpnn_pyg.py diff --git a/goli/nn/pyg_layers/pna_pyg.py b/graphium/nn/pyg_layers/pna_pyg.py similarity index 100% rename from goli/nn/pyg_layers/pna_pyg.py rename to graphium/nn/pyg_layers/pna_pyg.py diff --git a/goli/nn/pyg_layers/pooling_pyg.py b/graphium/nn/pyg_layers/pooling_pyg.py similarity index 100% rename from goli/nn/pyg_layers/pooling_pyg.py rename to graphium/nn/pyg_layers/pooling_pyg.py diff --git a/goli/nn/pyg_layers/utils.py b/graphium/nn/pyg_layers/utils.py similarity index 100% rename from goli/nn/pyg_layers/utils.py rename to graphium/nn/pyg_layers/utils.py diff --git a/goli/nn/residual_connections.py b/graphium/nn/residual_connections.py similarity index 100% rename from goli/nn/residual_connections.py rename to graphium/nn/residual_connections.py diff --git a/goli/nn/utils.py b/graphium/nn/utils.py similarity index 100% rename from goli/nn/utils.py rename to graphium/nn/utils.py diff --git a/goli/trainer/README.md b/graphium/trainer/README.md similarity index 100% rename from goli/trainer/README.md rename to graphium/trainer/README.md diff --git a/goli/trainer/__init__.py b/graphium/trainer/__init__.py similarity index 100% rename from goli/trainer/__init__.py rename to graphium/trainer/__init__.py diff --git a/goli/trainer/losses.py b/graphium/trainer/losses.py similarity index 100% rename from goli/trainer/losses.py rename to graphium/trainer/losses.py diff --git a/goli/trainer/metrics.py b/graphium/trainer/metrics.py similarity index 100% rename from goli/trainer/metrics.py rename to graphium/trainer/metrics.py diff --git a/goli/trainer/predictor.py b/graphium/trainer/predictor.py similarity index 100% rename from goli/trainer/predictor.py rename to graphium/trainer/predictor.py diff --git a/goli/trainer/predictor_options.py b/graphium/trainer/predictor_options.py similarity index 100% rename from goli/trainer/predictor_options.py rename to graphium/trainer/predictor_options.py diff --git a/goli/trainer/predictor_summaries.py b/graphium/trainer/predictor_summaries.py similarity index 100% rename from goli/trainer/predictor_summaries.py rename to graphium/trainer/predictor_summaries.py diff --git a/goli/utils/README.md b/graphium/utils/README.md similarity index 100% rename from goli/utils/README.md rename to graphium/utils/README.md diff --git a/goli/utils/__init__.py b/graphium/utils/__init__.py similarity index 100% rename from goli/utils/__init__.py rename to graphium/utils/__init__.py diff --git a/goli/utils/arg_checker.py b/graphium/utils/arg_checker.py similarity index 100% rename from goli/utils/arg_checker.py rename to graphium/utils/arg_checker.py diff --git a/goli/utils/command_line_utils.py b/graphium/utils/command_line_utils.py similarity index 100% rename from goli/utils/command_line_utils.py rename to graphium/utils/command_line_utils.py diff --git a/goli/utils/custom_lr.py b/graphium/utils/custom_lr.py similarity index 100% rename from goli/utils/custom_lr.py rename to graphium/utils/custom_lr.py diff --git a/goli/utils/decorators.py b/graphium/utils/decorators.py similarity index 100% rename from goli/utils/decorators.py rename to graphium/utils/decorators.py diff --git a/goli/utils/dict_tensor.py b/graphium/utils/dict_tensor.py similarity index 100% rename from goli/utils/dict_tensor.py rename to graphium/utils/dict_tensor.py diff --git a/goli/utils/fs.py b/graphium/utils/fs.py similarity index 100% rename from goli/utils/fs.py rename to graphium/utils/fs.py diff --git a/goli/utils/hashing.py b/graphium/utils/hashing.py similarity index 100% rename from goli/utils/hashing.py rename to graphium/utils/hashing.py diff --git a/goli/utils/moving_average_tracker.py b/graphium/utils/moving_average_tracker.py similarity index 100% rename from goli/utils/moving_average_tracker.py rename to graphium/utils/moving_average_tracker.py diff --git a/goli/utils/mup.py b/graphium/utils/mup.py similarity index 100% rename from goli/utils/mup.py rename to graphium/utils/mup.py diff --git a/goli/utils/packing.py b/graphium/utils/packing.py similarity index 100% rename from goli/utils/packing.py rename to graphium/utils/packing.py diff --git a/goli/utils/read_file.py b/graphium/utils/read_file.py similarity index 100% rename from goli/utils/read_file.py rename to graphium/utils/read_file.py diff --git a/goli/utils/safe_run.py b/graphium/utils/safe_run.py similarity index 100% rename from goli/utils/safe_run.py rename to graphium/utils/safe_run.py diff --git a/goli/utils/spaces.py b/graphium/utils/spaces.py similarity index 100% rename from goli/utils/spaces.py rename to graphium/utils/spaces.py diff --git a/goli/utils/tensor.py b/graphium/utils/tensor.py similarity index 100% rename from goli/utils/tensor.py rename to graphium/utils/tensor.py diff --git a/goli/visualization/README.md b/graphium/visualization/README.md similarity index 100% rename from goli/visualization/README.md rename to graphium/visualization/README.md diff --git a/goli/visualization/__init__.py b/graphium/visualization/__init__.py similarity index 100% rename from goli/visualization/__init__.py rename to graphium/visualization/__init__.py diff --git a/goli/visualization/vis_utils.py b/graphium/visualization/vis_utils.py similarity index 100% rename from goli/visualization/vis_utils.py rename to graphium/visualization/vis_utils.py diff --git a/pyproject.toml b/pyproject.toml index 5fe8dfc9c..2635ebf05 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -55,7 +55,7 @@ namespaces = true [tool.black] line-length = 110 -target-version = ['py39', 'py310'] +target-version = ['py310', 'py311'] include = '\.pyi?$' [tool.pytest.ini_options]