diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 01998020..7b6cf4ed 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -7,30 +7,11 @@ on: branches: jobs: - security: - runs-on: ubuntu-latest - steps: - - name: Checkout - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - name: Perform gitleaks checks - run: | - # Download and check - curl -LJO https://github.com/gitleaks/gitleaks/releases/download/v8.18.2/gitleaks_8.18.2_linux_x64.tar.gz - curl -LJO https://github.com/gitleaks/gitleaks/releases/download/v8.18.2/gitleaks_8.18.2_checksums.txt - shasum -a 256 --ignore-missing --quiet -c gitleaks_8.18.2_checksums.txt - if [ $? != 0 ]; then exit 1; fi - # Extract gitleaks - tar -zxvf gitleaks_8.18.2_linux_x64.tar.gz gitleaks - # Run gitleaks - ./gitleaks detect \ - --config .gitleaks.toml \ - --gitleaks-ignore-path .gitleaksignore \ - --no-git quality: runs-on: ubuntu-latest steps: - name: Checkout - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 - name: Setting up PDM uses: pdm-project/setup-pdm@568ddd69406b30de1774ec0044b73ae06e716aa4 # v4 with: @@ -60,7 +41,7 @@ jobs: sudo add-apt-repository ppa:openslide/openslide sudo apt install -y openslide-tools - name: Checkout - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 with: lfs: true - name: Setting up PDM @@ -74,3 +55,42 @@ jobs: python-versions: ${{ matrix.python-version }} - name: Executing unit tests run: nox -s test + docs: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 + - name: Setting up PDM + uses: pdm-project/setup-pdm@568ddd69406b30de1774ec0044b73ae06e716aa4 # v4 + with: + python-version: "3.10" + architecture: x64 + - name: Setting up nox + uses: wntrblm/nox@5656fcedc31a1ea37d016e4d94d00185330cc528 # 2024.04.15 + with: + python-versions: "3.10" + - name: Configure Git Credentials + run: | + git config user.email "action@github.com" + git config user.name "GitHub Action" + - name: Building docs + run: nox -s docs -- deploy --update-aliases dev + security: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 + - name: Perform gitleaks checks + run: | + # Download and check + curl -LJO https://github.com/gitleaks/gitleaks/releases/download/v8.18.2/gitleaks_8.18.2_linux_x64.tar.gz + curl -LJO https://github.com/gitleaks/gitleaks/releases/download/v8.18.2/gitleaks_8.18.2_checksums.txt + shasum -a 256 --ignore-missing --quiet -c gitleaks_8.18.2_checksums.txt + if [ $? != 0 ]; then exit 1; fi + # Extract gitleaks + tar -zxvf gitleaks_8.18.2_linux_x64.tar.gz gitleaks + # Run gitleaks + ./gitleaks detect \ + --config .gitleaks.toml \ + --gitleaks-ignore-path .gitleaksignore \ + --no-git diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 7805b489..e540ccd2 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -13,7 +13,7 @@ jobs: deploy: runs-on: ubuntu-latest steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 with: fetch-depth: 0 - name: Setting up PDM diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index b3214f57..07bf4275 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -2,6 +2,7 @@ name: Release on: + workflow_dispatch: push: tags: - "*" @@ -13,7 +14,7 @@ jobs: id-token: write contents: write steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 - name: Setting up PDM uses: pdm-project/setup-pdm@568ddd69406b30de1774ec0044b73ae06e716aa4 # v4 with: diff --git a/README.md b/README.md index d30f8ac0..4cbbdf5f 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,18 @@
Installation ā¢
@@ -59,12 +63,12 @@ eva --version
## How To Use
-_eva_ can be used directly from the terminal as a CLI tool as follows:
+_`eva`_ can be used directly from the terminal as a CLI tool as follows:
```sh
eva {fit,predict,predict_fit} --config url/or/path/to/the/config.yaml
```
-When used as a CLI tool, `_eva_` supports configuration files (`.yaml`) as an argument to define its functionality.
+When used as a CLI tool, _`eva`_ supports configuration files (`.yaml`) as an argument to define its functionality.
Native supported configs can be found at the [configs](https://github.com/kaiko-ai/eva/tree/main/configs) directory
of the repo. Apart from cloning the repo, you can download the latest config folder as `.zip` from your browser from
[here](https://download-directory.github.io/?url=https://github.com/kaiko-ai/eva/tree/main/configs). Alternatively,
@@ -98,7 +102,7 @@ and [tutorials](https://kaiko-ai.github.io/eva/dev/user-guide/advanced/replicate
## Benchmarks
-In this section you will find model benchmarks which were generated with `_eva_`.
+In this section you will find model benchmarks which were generated with _`eva`_.
### Table I: WSI patch-level benchmark
@@ -129,15 +133,15 @@ over 5 runs, with an average standard deviation of Ā±0.003._
_References_:
-1. _"Emerging properties in self-supervised vision transformersā_
-2. _"Benchmarking self-supervised learning on diverse pathology datasetsā_
-3. _"Scaling self-supervised learning for histopathology with masked image modelingā_
-4. _"A General-Purpose Self-Supervised Model for Computational Pathologyā_
-5. _"Towards Training Large-Scale Pathology Foundation Models: from TCGA to Hospital Scaleā_
+1. _"Emerging properties in self-supervised vision transformersā_, [arXiv](https://arxiv.org/abs/2104.14294)
+2. _"Benchmarking self-supervised learning on diverse pathology datasetsā_, [arXiv](https://arxiv.org/abs/2212.04690)
+3. _"Scaling self-supervised learning for histopathology with masked image modelingā_, [medRxiv](https://www.medrxiv.org/content/10.1101/2023.07.21.23292757v1)
+4. _"A General-Purpose Self-Supervised Model for Computational Pathologyā_, [arXiv](https://arxiv.org/abs/2308.15474)
+5. _"Towards Training Large-Scale Pathology Foundation Models: from TCGA to Hospital Scaleā_, [arXiv](https://arxiv.org/pdf/2404.15217)
## Contributing
-_eva_ is an open source project and welcomes contributions of all kinds. Please checkout the [developer](./docs/DEVELOPER_GUIDE.md)
+_`eva`_ is an open source project and welcomes contributions of all kinds. Please checkout the [developer](./docs/DEVELOPER_GUIDE.md)
and [contributing guide](./docs/CONTRIBUTING.md) for help on how to do so.
All contributors must follow the [code of conduct](./docs/CODE_OF_CONDUCT.md).
@@ -162,7 +166,23 @@ Our codebase is built using multiple opensource contributions