Docs

.github/workflows/docs.yaml

@@ -0,0 +1,51 @@
+name: website
+
+# build the documentation whenever there are new commits on main
+on:
+  push:
+    branches:
+      - main
+    # Alternative: only build for tags.
+    # tags:
+    #   - '*'
+
+# security: restrict permissions for CI jobs.
+permissions:
+  contents: read
+
+jobs:
+  # Build the documentation and upload the static HTML files as an artifact.
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      # ADJUST THIS: install all dependencies (including pdoc)
+      - run: pip install -e .
+      - run: pip install pdoc
+      # ADJUST THIS: build your documentation into docs/.
+      # We use a custom build script for pdoc itself, ideally you just run `pdoc -o docs/ ...` here.
+      # - run: python docs/make.py
+      - run: pdoc -d google -o docs/ HLAfreq
+
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/
+
+  # Deploy the artifact to GitHub pages.
+  # This is a separate job so that only actions/deploy-pages has the necessary permissions.
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -2,3 +2,6 @@ data/
 writeup/
 *__pycache__/
 *.code-workspace
+envs/.venv
+build/
+dist/

README.md

@@ -10,6 +10,8 @@ ability to mount an immune response to specific epitopes.
 Automated download of allele frequency data download from 
 [allele frequencies.net](http://www.allelefrequencies.net/).
 
+Source code is available at [Vaccitech/HLAfreq](https://github.com/Vaccitech/HLAfreq).
+
 ## Details
 Estimates are combined by modelling allele frequency as a 
 Dirichlet distribution which defines the probability of drawing each
@@ -21,7 +23,7 @@ for example population size when averaging across countries.
 When selecting a panel of HLA alleles to represent a population,
 allele frequency is not the only thing to consider. Depending on
 the purpose of the panel, you should include a range of loci and
-supertypes (groups alleles sharing binding specificies).
+supertypes (grouped alleles sharing binding specificies).
 
 ## Install
 `HLAfreq` is a `python` package available on windows, mac, and linux. We recommend installing
@@ -71,7 +73,7 @@ to get started with pip. If you do have issues with pip,
 try installing with conda as described above.
 
 ## Minimal example
-Download HLA data using `makeURL()` and `getAFdata()`.
+Download HLA data using `HLAfreq.HLAfreq.makeURL()` and `HLAfreq.HLAfreq.getAFdata()`.
 All arguments that can be specified in the webpage form are available,
 see `help(HLAfreq.makeURL)` for details (press `q` to exit).
 ```
@@ -83,7 +85,8 @@ aftab = HLAfreq.getAFdata(base_url)
 After downloading the data, it must be filtered so that all studies
 sum to allele frequency 1 (within tolerence). Then we must ensure
 that all studies report alleles at the same resolution.
-Finaly we can combine frequency estimates.
+Finaly we can combine frequency estimates, for more details see
+the `HLAfreq.HLAfreq.combineAF()` api documentation.
 ```
 aftab = HLAfreq.only_complete(aftab)
 aftab = HLAfreq.decrease_resolution(aftab, 2)
@@ -100,18 +103,27 @@ For more detailed walkthroughs see [HLAfreq/examples](https://github.com/Vaccite
 
 ## Docs
 For help on specific functions view the docstring, `help(function_name)`.
-Full documentation API at [HLAfreq/docs](https://github.com/Vaccitech/HLAfreq/blob/main/docs/HLAfreq.md)
-created with pdoc3 in pdf mode.
+Full documentation API at [HLAfreq/docs](https://vaccitech.github.io/HLAfreq/HLAfreq.html).
+Run `pdoc -d google -o docs/ HLAfreq` to generate the
+documentation in `./docs`.
+<!-- Documentation generated by pdoc should not be commited
+as it is auto generated by a github action. -->
+
 
 <!-- ## Developer notes
 # Install in dev mode
 pip install -e HLAfreq
+pip install -e .
 
 Update version in setup.py
 
-Update documentation with `pdoc --pdf -o docs/ src/HLAfreq/ > docs/HLAfreq.md`.
+Update documentation with: `pdoc -d google -o docs/ HLAfreq`.
+Note that github actions will automatically run this when pushed
+to `main` branch.
 
-Run tests `pytest` 
+Run tests `pytest`
+Or allow nox to do it `nox`. Nox will also run linting.
+On push github actions will run linting and pytest
 
 # Clear old build info
 rm -rf build dist src/*.egg-info