PFHub CLI tool

.github/workflows/flake-check.yml

@@ -0,0 +1,36 @@
+# Nix flake checker determines the health of the flake.lock files.
+# See https://determinate.systems/posts/flake-checker for some
+# explanation. This checks that the branches that are relied on for
+# packages are maintained and have recent commits. If they aren't
+# maintained then the checker will notify us and we can update the
+# lock or flake files.
+---
+name: Test Flakes
+on: [push, pull_request]
+jobs:
+  test-flakes:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install Nix
+        uses: DeterminateSystems/nix-installer-action@v4
+
+      - name: Check Nix flake inputs (./_data/python-pfhub/flake.lock)
+        uses: DeterminateSystems/flake-checker-action@v5
+        with:
+          flake-lock-path: _data/python-pfhub/flake.lock
+      - name: Build Nix package
+        run: |
+          cd _data/python-pfhub
+          nix develop # shoud be nix build, but linkml needs work
+          cd $GITHUB_WORKSPACE
+
+      - name: Check Nix flake inputs (./flake.lock)
+        uses: DeterminateSystems/flake-checker-action@v5
+      - name: Build Nix package
+        run: |
+          nix flake lock --update-input pfhub
+          nix build

.github/workflows/surge.yml

@@ -29,12 +29,12 @@ jobs:
       - run: echo "REPO=$(cat repo)" >> $GITHUB_ENV
       - run: echo "HEAD_REF=$(cat head_ref)" >> $GITHUB_ENV
 
-      - uses: actions/checkout@v2.3.4
+      - uses: actions/checkout@v3
         with:
           repository: ${{ env.REPO }}
           ref: ${{ env.HEAD_REF }}
 
-      - uses: cachix/install-nix-action@v14.1
+      - uses: cachix/install-nix-action@v20
         with:
           nix_path: nixpkgs=channel:nixos-unstable
 
@@ -50,7 +50,7 @@ jobs:
           SURGE_LOGIN: "${{ secrets.SURGE_LOGIN }}"
           SURGE_TOKEN: "${{ secrets.SURGE_TOKEN }}"
         run: |
-          nix-shell shell-surge.nix --command " \
+          nix develop --command bash -c " \
             if [[ ${{ env.NAME }} == 'pullrequest' ]]; then \
               rm -rf ./_site && \
               jekyll build && \

.github/workflows/test-conda.yml

@@ -0,0 +1,23 @@
+---
+name: Test PFHub With Conda
+on: [push, pull_request]
+jobs:
+  pfhub-conda-test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./_data/python-pfhub
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-name: test-env
+          create-args: >-
+            python=3.10
+      - run: python setup.py install
+      - run: py.test --nbval-lax --cov-fail-under=100
+      - run: |
+          mkdir -p tmp
+          cd tmp
+          pfhub test

.github/workflows/test-jekyll.yml

@@ -0,0 +1,35 @@
+---
+name: Test Jekyll
+on: [push, pull_request]
+jobs:
+  pfhub-nix-test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./
+    steps:
+      - uses: actions/checkout@v3
+      - uses: cachix/install-nix-action@v20
+        with:
+          nix_path: nixpkgs=channel:nixos-unstable
+          name: pfhub
+          authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
+          extraPullNames: nix-community
+      - run: echo "UID=${UID}" >> $GITHUB_ENV
+      - uses: actions/cache/restore@v3
+        with:
+          path: /run/user/${{ env.UID }}/http_cache.sqlite
+          key: ${{ runner.os}}-http_cache.sqlite
+      # Following required because of
+      # https://github.com/NixOS/nix/issues/3978#issuecomment-1585001299
+      - run: nix flake lock --update-input pfhub
+      - run: nix develop --command bash -c "make simulations"
+      - run: nix develop --command bash -c "find . -name '*.ipynb' -type f -not -path '*/.ipynb_checkpoints/*' -exec touch {} \;"
+      - run: nix develop --command bash -c "make notebooks"
+      - run: nix develop --command bash -c "rm -rf ./_site"
+      - run: nix develop --command bash -c "jekyll build -d ./_site/pfhub"
+      - uses: actions/cache/save@v3
+        if: always()
+        with:
+          path: /run/user/${{ env.UID }}/http_cache.sqlite
+          key: ${{ runner.os}}-http_cache.sqlite

.github/workflows/test-pfhub-package.yml

@@ -8,8 +8,8 @@ jobs:
       run:
         working-directory: ./_data/python-pfhub
     steps:
-      - uses: actions/checkout@v2.3.4
-      - uses: cachix/install-nix-action@v14.1
+      - uses: actions/checkout@v3
+      - uses: cachix/install-nix-action@v20
         with:
           nix_path: nixpkgs=channel:nixos-unstable
           name: pfhub
@@ -20,12 +20,12 @@ jobs:
         with:
           path: /run/user/${{ env.UID }}/http_cache.sqlite
           key: ${{ runner.os}}-http_cache.sqlite
-      - run: nix-shell --pure --command "py.test --nbval-lax --cov-fail-under=100"
-      - run: nix-shell --pure --command "black --check setup.py pfhub"
-      - run: nix-shell --pure --command "pylint setup.py pfhub"
-      - run: nix-shell --pure --command "flake8 setup.py pfhub"
-      - run: nix-shell --pure --command "cd ../../results; make notebooks"
-      - run: nix-shell --pure --command "py.test --nbval-lax ../../results/benchmark*.ipynb"
+      - run: nix develop --command bash -c "py.test --nbval-lax --cov-fail-under=100"
+      - run: nix develop --command bash -c "black --check setup.py pfhub"
+      - run: nix develop --command bash -c "pylint setup.py pfhub"
+      - run: nix develop --command bash -c "flake8 setup.py pfhub"
+      - run: nix develop --command bash -c "cd ../../results; make notebooks"
+      - run: nix develop --command bash -c "py.test --nbval-lax ../../results/benchmark*.ipynb"
       - uses: actions/cache/save@v3
         if: always()
         with:

.gitignore

@@ -15,3 +15,5 @@ benchmarks/.ipynb_checkpoints
 results/template.ipynb.md
 results/template.ipynb.raw.html
 results/*.ipynb
+_data/python-pfhub/dist
+_data/python-pfhub/build

DOCKER.md

@@ -18,21 +18,32 @@ Pull the Docker Instance from Dockerhub
 
 Run the container
 
-    $ docker run -i -t -p 4000:4000 wd15/pfhub:latest
+    $ docker run -i -t -p 8888:8888 wd15/pfhub:latest
 
-and then
+### View the notebooks
 
-    # nix-shell
     # cd pfhub
-    # jekyll serve --host 0.0.0.0
+    # jupyter-notebook --ip 0.0.0.0 --no-browser
 
-to view the website at http://127.0.0.1:4000/pfhub/ on the host.
+and view the running Jupyter file browser at http://127.0.0.1:8888 on
+the host.
+
+### View the website
+
+    # cd pfhub
+    # jekyll serve --host 0.0.0.0 --port 8888
+
+to view the website at http://127.0.0.1:8888/pfhub/ on the host.
 
 ## Build the Docker instance
 
-Clone this repository and run
+The Docker instance is built using Nix. See (./NIX.md) to get started.
+Once you're familiar with Nix, clone this repository and then
+
+    $ nix build .#docker
+    $ docker load < result
 
-    $ docker build -t wd15/pfhub:latest .
+in the base directory.
 
 ## Push the Docker instance