Merge branch 'main' into openmm

haddocking · Sep 23, 2024 · da177d4 · da177d4
2 parents ff3e980 + c6b3f99
commit da177d4
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diff --git a/.github/workflows/ci.yml b/.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
diff --git a/.github/workflows/docs.yml b/.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
diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
@@ -26,15 +26,7 @@ jobs:
       # needs to install hd3 so the command-line pages are
       # rendered properly
       - name: Install HADDOCK3
-        run: |
-          pwd
-          ls -lsa
-          mkdir bin
-          touch bin/cns
-          cd src/fcc/src
-          chmod u+x Makefile
-          ./Makefile 2>%1 >/dev/null || true
-          cd -
+        run: pip install -v .
 
       - name: Generate docs
         run: |

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
diff --git a/.gitignore b/.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
diff --git a/.gitmodules b/.gitmodules
diff --git a/MANIFEST.in b/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/*
diff --git a/examples/docking-protein-glycan/docking-flexref-protein-glycan-full.cfg b/examples/docking-protein-glycan/docking-flexref-protein-glycan-full.cfg
@@ -42,8 +42,7 @@ mdsteps_cool1 = 5000
 mdsteps_cool2 = 10000
 mdsteps_cool3 = 10000
 ambig_fname = "data/ambig.tbl"
-# give full flexibilit to the glycan
-nfle = 1
+# give full flexibility to the glycan
 fle_sta_1 = 1
 fle_end_1 = 4
 fle_seg_1 = "B"

diff --git a/examples/docking-protein-glycan/docking-flexref-protein-glycan-test.cfg b/examples/docking-protein-glycan/docking-flexref-protein-glycan-test.cfg
@@ -38,8 +38,7 @@ mdsteps_cool1 = 5000
 mdsteps_cool2 = 10000
 mdsteps_cool3 = 10000
 ambig_fname = "data/ambig.tbl"
-# give full flexibilit to the glycan
-nfle = 1
+# give full flexibility to the glycan
 fle_sta_1 = 1
 fle_end_1 = 4
 fle_seg_1 = "B"

diff --git a/examples/docking-protein-homotrimer/docking-protein-homotrimer-full.cfg b/examples/docking-protein-homotrimer/docking-protein-homotrimer-full.cfg
@@ -41,7 +41,6 @@ ambig_fname = "data/1qu9_whiscy_air.tbl"
 sampling = 2000
 # Define CNS restraints between molecules
 ncs_on = true
-numncs = 2
 ncs_sta1_1=2
 ncs_end1_1=128
 ncs_seg1_1="A"
@@ -56,7 +55,6 @@ ncs_end2_2=128
 ncs_seg2_2="C"
 # Define C3 symmetry restraints
 sym_on = true
-numc3sym = 1
 c3sym_sta1_1=2
 c3sym_end1_1=128
 c3sym_seg1_1="A"
@@ -79,7 +77,6 @@ tolerance = 5
 ambig_fname = "data/1qu9_whiscy_air.tbl"
 # Define NCS restraints between molecules
 ncs_on = true
-numncs = 2
 ncs_sta1_1=2
 ncs_end1_1=128
 ncs_seg1_1="A"
@@ -94,7 +91,6 @@ ncs_end2_2=128
 ncs_seg2_2="C"
 # Define C3 symmetry restraints
 sym_on = true
-numc3sym = 1
 c3sym_sta1_1=2
 c3sym_end1_1=128
 c3sym_seg1_1="A"
@@ -113,7 +109,6 @@ tolerance = 5
 ambig_fname = "data/1qu9_whiscy_air.tbl"
 # Define NCS restraints between molecules
 ncs_on = true
-numncs = 2
 ncs_sta1_1=2
 ncs_end1_1=128
 ncs_seg1_1="A"
@@ -128,7 +123,6 @@ ncs_end2_2=128
 ncs_seg2_2="C"
 # Define C3 symmetry restraints
 sym_on = true
-numc3sym = 1
 c3sym_sta1_1=2
 c3sym_end1_1=128
 c3sym_seg1_1="A"

diff --git a/examples/docking-protein-homotrimer/docking-protein-homotrimer-test.cfg b/examples/docking-protein-homotrimer/docking-protein-homotrimer-test.cfg
@@ -36,7 +36,6 @@ ambig_fname = "data/1qu9_whiscy_air.tbl"
 sampling = 20
 # Define NCS restraints between molecules
 ncs_on = true
-numncs = 2
 ncs_sta1_1=2
 ncs_end1_1=128
 ncs_seg1_1="A"
@@ -51,7 +50,6 @@ ncs_end2_2=128
 ncs_seg2_2="C"
 # Define C3 symmetry restraints
 sym_on = true
-numc3sym = 1
 c3sym_sta1_1=2
 c3sym_end1_1=128
 c3sym_seg1_1="A"
@@ -74,7 +72,6 @@ tolerance = 20
 ambig_fname = "data/1qu9_whiscy_air.tbl"
 # Define NCS restraints between molecules
 ncs_on = true
-numncs = 2
 ncs_sta1_1=2
 ncs_end1_1=128
 ncs_seg1_1="A"
@@ -89,7 +86,6 @@ ncs_end2_2=128
 ncs_seg2_2="C"
 # Define C3 symmetry restraints
 sym_on = true
-numc3sym = 1
 c3sym_sta1_1=2
 c3sym_end1_1=128
 c3sym_seg1_1="A"
@@ -108,7 +104,6 @@ tolerance = 20
 ambig_fname = "data/1qu9_whiscy_air.tbl"
 # Define NCS restraints between molecules
 ncs_on = true
-numncs = 2
 ncs_sta1_1=2
 ncs_end1_1=128
 ncs_seg1_1="A"
@@ -123,7 +118,6 @@ ncs_end2_2=128
 ncs_seg2_2="C"
 # Define C3 symmetry restraints
 sym_on = true
-numc3sym = 1
 c3sym_sta1_1=2
 c3sym_end1_1=128
 c3sym_seg1_1="A"

diff --git a/examples/docking-protein-peptide/docking-protein-peptide-cltsel-full.cfg b/examples/docking-protein-peptide/docking-protein-peptide-cltsel-full.cfg
@@ -51,7 +51,6 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 5
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle = 1
 fle_sta_1 = 1
 fle_end_1 = 11
 fle_seg_1 = "B"
@@ -72,7 +71,6 @@ reference_fname = "data/1nx1_refe.pdb"
 tolerance = 5
 ambig_fname = "data/ambig.tbl"
 # Define peptide as fully flexible
-nfle = 1
 fle_sta_1 = 1
 fle_end_1 = 11
 fle_seg_1 = "B"