Docs/v3

.github/workflows/cli.yml

@@ -299,9 +299,36 @@ jobs:
           ./tests/test-linux-distros ./.out/nextclade-x86_64-unknown-linux-gnu
 
 
+  check-cli-docs:
+    name: "Check that autogenerated CLI documentation is up-to-date"
+    needs: [ build-cli ]
+    runs-on: ubuntu-22.04
+
+    steps:
+      - name: "Checkout code"
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 1
+          submodules: true
+
+      - name: "Download build artifacts"
+        uses: actions/download-artifact@v3
+        with:
+          name: "out"
+          path: ".out"
+
+      - name: "Re-generate CLI docs"
+        run: |
+          chmod +x ./.out/nextclade-x86_64-unknown-linux-gnu
+          ./scripts/update_cli_reference_docs ./.out/nextclade-x86_64-unknown-linux-gnu
+
+      - name: "Check that the git diff is clean"
+        run: |
+          git -c color.ui=always diff --exit-code 'docs/user/nextclade-cli/reference.md' || (echo "Autogenerated CLI documentation is not up-to-date, please run './scripts/update_cli_reference_docs <path_to_nextclade>', then verify and commit the changes." >&2; exit 1)
+
   publish-to-github-releases:
     name: "Publish to GitHub Releases"
-    needs: [ build-cli, run-unit-tests, run-lints, run-smoke-tests, run-linux-distros-test ]
+    needs: [ build-cli, run-unit-tests, run-lints, run-smoke-tests, run-linux-distros-test, check-cli-docs ]
     if: endsWith(github.ref, '/release-cli')
     runs-on: ubuntu-22.04
 
@@ -337,7 +364,7 @@ jobs:
 
   publish-to-docker-hub:
     name: "Publish to Docker Hub"
-    needs: [ build-cli, run-unit-tests, run-lints, run-smoke-tests, run-linux-distros-test ]
+    needs: [ build-cli, run-unit-tests, run-lints, run-smoke-tests, run-linux-distros-test, check-cli-docs ]
     if: endsWith(github.ref, '/release-cli')
     runs-on: ubuntu-22.04
 

Makefile

@@ -52,10 +52,8 @@ docker-docs:
 	--name=nextclade-docs-builder-$(shell date +%s) \
 	--init \
 	--user=$(shell id -u):$(shell id -g) \
-	--volume=$(shell pwd):/home/user/src \
+	--volume=$(shell pwd):/workdir \
 	--publish=8000:8000 \
-	--workdir=/home/user/src \
-	--env 'TERM=xterm-256colors' \
 	nextclade-docs-builder
 
 

docs/Dockerfile

@@ -1,4 +1,6 @@
-FROM continuumio/miniconda3:4.9.2
+FROM continuumio/miniconda3
+
+SHELL ["bash", "--login", "-euxo", "pipefail", "-c"]
 
 ARG DEBIAN_FRONTEND=noninteractive
 ARG USER=user
@@ -9,8 +11,20 @@ ARG GID
 ENV TERM="xterm-256color"
 ENV HOME="/home/user"
 
+
+RUN set -euxo pipefail >/dev/null \
+&& export DEBIAN_FRONTEND=noninteractive \
+&& apt-get update -qq --yes \
+&& apt-get install -qq --no-install-recommends --yes \
+  make \
+  sudo \
+>/dev/null \
+&& apt-get clean autoclean >/dev/null \
+&& apt-get autoremove --yes >/dev/null \
+&& rm -rf /var/lib/apt/lists/*
+
 # Make a user and group
-RUN set -x >/dev/null \
+RUN set -euxo pipefail >/dev/null \
 && \
   if [ -z "$(getent group ${GID})" ]; then \
     addgroup --system --gid ${GID} ${GROUP}; \
@@ -34,27 +48,18 @@ RUN set -x >/dev/null \
 && echo "%sudo ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers \
 && echo "${USER} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers \
 && touch ${HOME}/.hushlogin \
-&& chown -R ${UID}:${GID} "${HOME}"
-
-RUN set -x \
-  && chown -R ${USER}:${GROUP} ${HOME}
+&& chown -R ${UID}:${GID} "${HOME}" \
+&& chown -R ${USER}:${GROUP} ${HOME}
 
-COPY environment.yml ${HOME}/src/
+WORKDIR /workdir
 
-WORKDIR ${HOME}/src
+COPY environment.yml /workdir
 
-RUN set -x \
-  && conda env create docs.clades.nextstrain.org
+RUN set -euxo pipefail >/dev/null \
+  && conda env create -n "docs.clades.nextstrain.org"
 
 USER ${USER}
 
-RUN set -x \
-  && conda init bash \
-  && echo "conda activate docs.clades.nextstrain.org" >> ${HOME}/.bashrc
+ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "docs.clades.nextstrain.org", "bash", "-euo", "pipefail", "-c"]
 
-CMD bash -c "set -x \
-  && source ${HOME}/.bashrc \
-  && cd ${HOME}/src/docs \
-  && rm -rf build \
-  && make autobuild \
-  "
+CMD ["cd docs && make autobuild"]

docs/_static/css/custom.css

@@ -22,3 +22,7 @@ details pre * {
   white-space: pre-wrap;
   word-wrap: break-word;
 }
+
+.rst-content code {
+  font-size: 0.8em !important;
+}