Generate docs and schema with github actions

.github/workflows/build.yml

@@ -0,0 +1,51 @@
+name: Test and Deploy bioimageio.spec
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install tox tox-gh-actions
+    - name: Test with tox
+      run: tox
+
+  deploy:
+    runs-on: ubuntu-latest
+    needs: test
+    if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.7
+    - name: Install dependencies
+      run: |
+        pip install .
+    - run: mkdir ./dist && cp ./bioimageio_rdf_spec.md ./dist # TODO: remove this when we generate the RDF docs
+    - name: Generate Docs
+      run: python scripts/generate_docs.py
+    # - name: Generate JSON Schema # TODO: fix this
+    #   run: python scripts/generate_json_specs.py
+    - name: Deploy Docs and Schema 🚀
+      uses: JamesIves/[email protected]
+      with:
+        branch: gh-pages
+        folder: dist

.gitignore

@@ -2,3 +2,4 @@ __pycache__/
 .vscode
 tmp
 *.egg-info/
+dist

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ repos:
     hooks:
     - id: generate docs
       name: generate docs
-      entry: python scripts/gen_spec_doc.py
+      entry: python scripts/generate_docs.py
       language: system
       always_run: true
       pass_filenames: false

README.md

@@ -16,17 +16,17 @@ As a general guideline, please follow the model RDF spec to describe AI models a
 
 A BioImage.IO-compatible Resource Description File (RDF) is a YAML file with a set of specifically defined fields. You can find detaialed field definition and examples here in the [generic RDF spec](./bioimageio_rdf_spec.md).
 
-## [Model Resource Description File Specification](./generated/bioimageio_model_spec.md)
+## [Model Resource Description File Specification](https://github.com/bioimage-io/spec-bioimage-io/blob/gh-pages/bioimageio_model_spec.md)
 
-Besides the generic RDF spec, the [`Model Resource Description File Specification`](./generated/bioimageio_model_spec.md)(`model RDF`) defines a file format for representing pretrained AI models in [YAML format](https://en.wikipedia.org/wiki/YAML). This format is used to describe models hosted on the [BioImage.IO](https://bioimage.io) model repository site.
+Besides the generic RDF spec, the [`Model Resource Description File Specification`](https://github.com/bioimage-io/spec-bioimage-io/blob/gh-pages/bioimageio_model_spec.md)(`model RDF`) defines a file format for representing pretrained AI models in [YAML format](https://en.wikipedia.org/wiki/YAML). This format is used to describe models hosted on the [BioImage.IO](https://bioimage.io) model repository site.
 
 Here is a list of model RDF Examples:
  - [UNet 2D Nuclei Broad](https://github.com/bioimage-io/pytorch-bioimage-io/blob/master/specs/models/unet2d_nuclei_broad/UNet2DNucleiBroad.model.yaml).
 
 
 ## Recommendations
 
- * For AI models, consider using the model-specific spec (i.e. [model RDF](./generated/bioimageio_model_spec.md)) instead of the generic RDF. Only fallback to the generic RDF if writing model specific RDF is not possible for some reason.
+ * For AI models, consider using the model-specific spec (i.e. [model RDF](https://github.com/bioimage-io/spec-bioimage-io/blob/gh-pages/bioimageio_model_spec.md)) instead of the generic RDF. Only fallback to the generic RDF if writing model specific RDF is not possible for some reason.
  * The RDF or package file name should not contain spaces or special characters, it should be concise, descriptive, in kebab case or camel case.
  * Due to the limitations of storage services such as Zenodo, which does not support subfolders, it is recommended to place other files in the same directory level of the RDF file and try to avoid using subdirectories.
  * Use the [bioimage.io spec validator](#bioimageio-spec-validator) to verify your YAML file
@@ -46,7 +46,7 @@ TODO from pip/conda
 pip install git+https://github.com/bioimage-io/spec-bioimage-io
 ```
 
-To use the spec validator, you can verify a model configuration in the [bioimage.io model format](./generated/bioimageio_model_spec.md) using the following command:
+To use the spec validator, you can verify a model configuration in the [bioimage.io model format](https://github.com/bioimage-io/spec-bioimage-io/blob/gh-pages/bioimageio_model_spec.md) using the following command:
 ```
 python -m bioimageio.spec verify-spec <MY-MODEL>.model.yaml
 ```

bioimageio_rdf_spec.md

@@ -46,7 +46,7 @@ The common fields for all the resource description files are:
 
 ## Describing AI models
 
-In general, it is discouraged to use the generic RDF to describe AI models and we recommend to follow the [model RDF spec](generated/bioimageio_model_spec.md) instead. However, in some cases, it is not possible to provide detailed fields defined in the [model RDF spec](generated/bioimageio_model_spec.md), the generic RDF can be used for discribing AI models.
+In general, it is discouraged to use the generic RDF to describe AI models and we recommend to follow the [model RDF spec](https://github.com/bioimage-io/spec-bioimage-io/blob/gh-pages/bioimageio_model_spec.md) instead. However, in some cases, it is not possible to provide detailed fields defined in the [model RDF spec](https://github.com/bioimage-io/spec-bioimage-io/blob/gh-pages/bioimageio_model_spec.md), the generic RDF can be used for discribing AI models.
 
 To do that, you need to first set the `type` filed to `model`.