Merge branch 'develop' into no_priors

.github/workflows/deploy_dockerhub.yml

@@ -2,13 +2,29 @@
 name: Deploy to dockerhub
 on: [push, workflow_dispatch]
 jobs:
+  check-secret:
+    runs-on: ubuntu-latest
+    outputs:
+      secrets-defined: ${{ steps.secret-check.outputs.defined }}
+    steps:
+      - name: Check for Secret availability
+        id: secret-check
+        shell: bash
+        run: |
+          if [ "${{ secrets.DOCKER_USERNAME }}" != '' ]; then
+            echo "defined=true" >> $GITHUB_OUTPUT;
+          else
+            echo "defined=false" >> $GITHUB_OUTPUT;
+          fi
+
   build:
     name: Deploy to dockerhub
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@master
     - run: git archive -v -o container/charliecloud/parpe_base/parpe.tar.gz --format=tar.gz HEAD
     - name: Publish to Registry
+      if: needs.check-secret.outputs.secrets-defined == 'true'
       uses: elgohr/Publish-Docker-Github-Action@v5
       with:
         name: dweindl/parpe

deps/AMICI/python/sdist/pyproject.toml

@@ -2,13 +2,7 @@
 requires = [
     "setuptools>=40.6.3",
     "wheel",
-    # oldest-supported-numpy helps us to pin numpy here to the lowest supported
-    # version to have ABI-compatibility with the numpy version in the runtime
-    # environment. The undesirable alternative would be pinning the setup.py
-    # numpy requirement to the same version as here, which we want to avoid.
-    # cf. discussion at https://github.com/numpy/numpy/issues/5888
-    # (https://github.com/scipy/oldest-supported-numpy/)
-    "oldest-supported-numpy",
+    "numpy>=2.0",
     "cmake-build-extension==0.5.1",
 ]
 build-backend = "setuptools.build_meta"

deps/AMICI/python/sdist/setup.py

@@ -131,7 +131,9 @@ def get_extensions():
         cmake_configure_options=[
             *global_cmake_configure_options,
             "-Werror=dev"
-            if "GITHUB_ACTIONS" in os.environ
+            # Turn warnings in to errors on GitHub Actions,
+            #  match original repo and forks with default name
+            if os.environ.get("GITHUB_REPOSITORY", "").endswith("/AMICI")
             else "-Wno-error=dev",
             "-DAMICI_PYTHON_BUILD_EXT_ONLY=ON",
             f"-DPython3_EXECUTABLE={Path(sys.executable).as_posix()}",

doc/conf.py

@@ -55,7 +55,7 @@
     # 'recommonmark',
     'nbsphinx',
     'IPython.sphinxext.ipython_console_highlighting',
-    'm2r2',
+    'myst_parser',
 ]
 
 # Add any paths that contain templates here, relative to this directory.

doc/requirements_doc.txt

@@ -3,9 +3,10 @@ sphinx_rtd_theme>=1.2.0
 breathe>=4.35.0
 exhale>=0.2.3
 ipython>=8.13.2
-m2r2>=0.2.7
+myst-parser
 sphinx-autodoc-typehints>=1.10.3
 nbsphinx==0.9.1
+nbconvert>=7.1.0
 -e git+https://github.com/svenevs/exhale.git@a1a8551321e246e3ab81f5456e04a8159804595b#egg=exhale
 
 # to import parpe package:

python/parpe/hdf5_pe_input.py

@@ -1109,8 +1109,8 @@ def write_optimization_options(f: h5py.File) -> None:
     # set IpOpt options
     g = f.require_group('optimizationOptions/ipopt')
     g.attrs['max_iter'] = 100
-    g.attrs['hessian_approximation'] = np.string_("limited-memory")
-    g.attrs["limited_memory_update_type"] = np.string_("bfgs")
+    g.attrs['hessian_approximation'] = np.bytes_("limited-memory")
+    g.attrs["limited_memory_update_type"] = np.bytes_("bfgs")
     g.attrs["tol"] = 1e-9
     g.attrs["acceptable_iter"] = 1
     # set ridiculously high, so only the acceptable_* options below matter