re-work haddock3 installation

.github/workflows/ci.yml

@@ -0,0 +1,65 @@
+---
+name: ci
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  ci:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10"]
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y openmpi-bin libopenmpi3 libopenmpi-dev
+
+      - name: install test dependencies
+        run: >-
+          pip install coverage pytest pytest-cov hypothesis pytest-mock mypy
+          fastapi==0.110.1 httpx==0.27.0 mpi4py==3.1.6
+
+      - name: install haddock3
+        run: pip install -v .
+
+      ## Disabled for now until we figure out a good configuration ##
+      # - name: check types
+      #   run: mypy src/
+      ###############################################################
+
+      - name: run unit tests
+        run: >-
+          pytest tests/
+          --cov --cov-report=term-missing --cov-append
+          --hypothesis-show-statistics
+
+      - name: run integration tests
+        run: >-
+          pytest integration_tests/
+          --cov --cov-report=term-missing --cov-append
+          --hypothesis-show-statistics
+
+      - name: generate coverage report
+        run: |
+          coverage report
+          coverage xml
+
+      - uses: codacy/codacy-coverage-reporter-action@v1
+        if: >-
+          ${{ github.event_name != 'pull_request' ||
+          github.event.pull_request.head.repo.full_name == github.repository }}
+        with:
+          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+          coverage-reports: ./coverage.xml

.github/workflows/docs.yml

@@ -4,28 +4,25 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: [main]
 
 jobs:
   build:
-    runs-on: ${{ matrix.platform }}
-    strategy:
-      matrix:
-        platform: [ubuntu-latest, macos-latest]
-        python-version: [3.9]
+    runs-on: ubuntu-latest
 
     steps:
       - uses: actions/checkout@v2
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+      - uses: actions/setup-python@v2
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: 3.9
 
       - name: Install dependencies
         run: |
           python -m pip install pip==23.1.2 setuptools==67.7.2 wheel==0.40.0
           pip install virtualenv==20.23.0 tox==4.5.1.1
 
+      - name: install haddock3
+        run: pip install -v .
+
       - name: docs
         run: tox -e docs

.gitignore

@@ -154,6 +154,5 @@ docs/haddock.modules.rst
 docs/haddock.modules.base_cns_module.rst
 docs/setup.rst
 docs/clients/*rst
-src/fast-rmsdmatrix
-src/fcc
+src/haddock/bin/
 log

MANIFEST.in

@@ -34,3 +34,5 @@ recursive-include varia *.f
 recursive-include varia *.inc
 recursive-include varia *.lua
 recursive-include varia *.md
+
+include src/haddock/bin/*