Merge branch 'main' into fair

.github/workflows/github-to-gitlab-push-sync.yml

@@ -0,0 +1,23 @@
+name: build
+
+on:
+  push:
+    tags:
+      - '*'
+
+jobs:
+  sync:
+    runs-on: ubuntu-latest
+    name: sync to codehub
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: main
+          fetch-depth: 0
+
+      - uses: cniethammer/git-repo-sync@cb1067d118c0c209bcded585b5c78e581bb0dfec
+        with:
+          target-url: https://codehub.hlrs.de/coes/bioexcel/haddock3.git
+          target-username: ${{ secrets.ACCESS_TOKEN_NAME }}
+          target-token: ${{ secrets.ACCESS_TOKEN }}

.github/workflows/tests.yml

@@ -42,6 +42,11 @@ jobs:
           chmod u+x Makefile
           ./Makefile 2>%1 >/dev/null || true
           cd -
+          cd src/fast-rmsdmatrix/src
+          chmod u+x Makefile
+          make fast-rmsdmatrix
+          cd -
+
 
       - name: types
         run: tox -e types
@@ -58,6 +63,7 @@ jobs:
   integration:
     needs: unit
     runs-on: ubuntu-latest
+    if: ${{ github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository }}
     strategy:
       matrix:
         python-version: [3.9]
@@ -87,15 +93,15 @@ jobs:
           chmod u+x Makefile
           ./Makefile 2>%1 >/dev/null || true
           cd -
+          cd src/fast-rmsdmatrix/src
+          chmod u+x Makefile
+          make fast-rmsdmatrix
+          cd -
 
       - name: install integration dependencies
-        # developers outside the organization cannot access secrets
-        #   so we need to make sure that the job does not fail
-        # the test will handle the environment variable not being set
-        #  and will skip the test
-        continue-on-error: true
         run: |
           curl ${{ secrets.CNS_LINK }} -o $CNS_EXEC -s
           chmod +x $CNS_EXEC
 
-      - run: tox -e integration
+      - name: run integration tests
+        run: tox -e integration

.gitignore

@@ -145,7 +145,12 @@ examples/*/capriscoring-test/*
 examples/thirdparty/*/run*
 
 # ignore generated data for docs
-docs/modules/*/params/*.rst
-docs/modules/general_module_params.rst
-docs/reference/core/mandatory_parameters.rst
 haddock3-docs/
+docs/modules/**/*.rst
+docs/reference/**/*rst
+docs/modules.rst
+docs/haddock.rst
+docs/haddock.modules.rst
+docs/haddock.modules.base_cns_module.rst
+docs/setup.rst
+docs/clients/*rst

.gitmodules

@@ -1,3 +1,7 @@
 [submodule "src/fcc"]
 	path = src/fcc
 	url = https://github.com/haddocking/fcc.git
+
+[submodule "src/fast-rmsdmatrix"]
+	path = src/fast-rmsdmatrix
+	url = https://github.com/mgiulini/fast-rmsdmatrix.git

README.md

@@ -8,6 +8,7 @@ stable beta version.
 [![docs](https://github.com/haddocking/haddock3/workflows/pages/badge.svg?branch=main)](https://github.com/haddocking/haddock3/actions?workflow=pages)
 [![Research Software Directory](https://img.shields.io/badge/rsd-haddock3-00a3e3.svg)](https://research-software-directory.org/software/haddock3)
 [![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8B%20%20%E2%97%8B%20%20%E2%97%8B-orange)](https://fair-software.eu)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10527751.svg)](https://doi.org/10.5281/zenodo.10527751)
 
 * * *