Update Dependencies

.github/workflows/ci.yml

@@ -19,14 +19,11 @@ jobs:
           - os: ubuntu-latest
             python: "3.13"
             toxenv: base
-          #- os: ubuntu-latest
-          #  python: "3.12"
-          #  toxenv: base
           - os: ubuntu-latest
-            python: "3.11"
+            python: "3.12"
             toxenv: base
           - os: ubuntu-latest
-            python: "3.10"
+            python: "3.11"
             toxenv: base
           - os: ubuntu-latest
             python: "3.11"
@@ -68,9 +65,9 @@ jobs:
             toxenv: external-notebooks
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python }}
           cache: pip
@@ -79,18 +76,28 @@ jobs:
         if: ${{ startsWith(matrix.toxenv, 'external-') }}
         uses: julia-actions/setup-julia@v2
         with:
-          version: "1.11"
+          version: "1"  # Use the latest stable Julia version
 
       - name: Install Julia dependencies
         if: ${{ startsWith(matrix.toxenv, 'external-') }}
-        run: julia -e 'using Pkg; Pkg.add("PyCall")'
+        env:
+          # make Julia/PyCall bind to the same Python used by the job
+          PYTHON: ${{ env.pythonLocation }}/bin/python
+        run: |
+          julia -e 'using Pkg; Pkg.add("PyCall")'
+
+      - name: Install R
+        if: ${{ startsWith(matrix.toxenv, 'external-') }}
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
 
       - name: Install dependencies
         run: |
           case "${{ matrix.toxenv }}" in
-            base|visualization|mac|base-notebooks) .github/workflows/install_deps.sh base R ;;
+            base|visualization|mac|base-notebooks) .github/workflows/install_deps.sh base ;;
             petab) .github/workflows/install_deps.sh amici ;;
-            external-*) .github/workflows/install_deps.sh base R amici ;;
+            external-*) .github/workflows/install_deps.sh base amici ;;
             lint|project|doc|migrate) .github/workflows/install_deps.sh doc ;;
           esac
           python -m pip install -U pip tox
@@ -100,8 +107,9 @@ jobs:
 
       # If each tox env generates coverage.xml, include flags; otherwise combine explicitly
       - name: Upload coverage
-        if: ${{ always() && matrix.os == 'ubuntu-latest' }}  # optional
-        uses: codecov/codecov-action@v4
+        if: ${{ always() && matrix.os == 'ubuntu-latest' }}
+        uses: codecov/codecov-action@v6
+        continue-on-error: true
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage.xml

.github/workflows/deploy.yml

@@ -14,10 +14,10 @@ jobs:
 
     steps:
       - name: Check out repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Prepare Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.12"
           cache: pip

.github/workflows/install_deps.sh

@@ -48,29 +48,10 @@ install_base() {
   fi
 }
 
-install_r() {
-  log_info "Installing R..."
-  if is_macos; then
-    brew install r
-  else
-    # Prefer distro packages in CI
-    apt_install libtirpc-dev r-base r-base-dev
-    # Make R shared libs discoverable for the rest of the job
-    export_env_var LD_LIBRARY_PATH "${LD_LIBRARY_PATH:-/usr/lib}:/usr/lib/R/lib:/usr/local/lib/R/lib"
-  fi
-
-  if command -v R >/dev/null 2>&1; then
-    log_info "R installed: $(R --version | head -n1)"
-  else
-    log_error "R installation failed (R not on PATH)"
-    exit 1
-  fi
-}
-
 install_amici() {
   log_info "Installing AMICI dependencies..."
   if ! is_macos; then
-    apt_install swig libatlas-base-dev libhdf5-serial-dev libboost-all-dev
+    apt_install libhdf5-serial-dev libboost-all-dev
   fi
   log_info "Installing AMICI Python package..."
   python -m pip uninstall -y amici pyabc || true
@@ -93,7 +74,6 @@ install_dev_tools() {
 
 install_all() {
   install_base
-  install_r
   install_amici
   install_doc_tools
   install_dev_tools
@@ -105,7 +85,6 @@ Usage: $0 [OPTION]...
 
 Options:
   base        Install base dependencies (Redis)
-  R           Install R (Ubuntu: apt; macOS: brew)
   amici       Install AMICI dependencies
   doc         Install documentation tools (Pandoc)
   dev         Install development tools
@@ -124,7 +103,6 @@ main() {
   for arg in "$@"; do
     case "$arg" in
       base)  install_base ;;
-      R)     install_r ;;
       amici) install_amici ;;
       doc)   install_doc_tools ;;
       dev)   install_dev_tools ;;

.pre-commit-config.yaml

@@ -61,7 +61,7 @@ repos:
 
 # Configuration
 default_language_version:
-  python: python3.11
+  python: python3.13
 
 # Global exclusions
 exclude: |

CHANGELOG.rst

@@ -7,6 +7,14 @@ Release Notes
 0.12 Series
 ...........
 
+0.12.18 (2026-04-14)
+--------------------
+
+General:
+
+* Support of amici 1.0.0
+* Remove support for python 3.10
+
 0.12.17 (2026-02-24)
 --------------------
 

doc/examples/model_selection.ipynb

@@ -83,7 +83,7 @@
     "    # sample from a gaussian\n",
     "    y = st.norm(parameters.x, sigma).rvs()\n",
     "    # return the sample as dictionary\n",
-    "    return {\"y\": y}"
+    "    return {'y': y}"
    ]
   },
   {
@@ -110,8 +110,8 @@
     "# Their mean differs.\n",
     "mu_x_1, mu_x_2 = 0, 1\n",
     "parameter_priors = [\n",
-    "    pyabc.Distribution(x=pyabc.RV(\"norm\", mu_x_1, sigma)),\n",
-    "    pyabc.Distribution(x=pyabc.RV(\"norm\", mu_x_2, sigma)),\n",
+    "    pyabc.Distribution(x=pyabc.RV('norm', mu_x_1, sigma)),\n",
+    "    pyabc.Distribution(x=pyabc.RV('norm', mu_x_2, sigma)),\n",
     "]"
    ]
   },
@@ -142,7 +142,7 @@
    "source": [
     "# We plug all the ABC options together\n",
     "abc = pyabc.ABCSMC(\n",
-    "    models, parameter_priors, pyabc.PercentileDistance(measures_to_use=[\"y\"])\n",
+    "    models, parameter_priors, pyabc.PercentileDistance(measures_to_use=['y'])\n",
     ")"
    ]
   },
@@ -176,8 +176,8 @@
     "# y_observed is the important piece here: our actual observation.\n",
     "y_observed = 1\n",
     "# and we define where to store the results\n",
-    "db_path = \"sqlite:///\" + os.path.join(tempfile.gettempdir(), \"test.db\")\n",
-    "history = abc.new(db_path, {\"y\": y_observed})"
+    "db_path = 'sqlite:///' + os.path.join(tempfile.gettempdir(), 'test.db')\n",
+    "history = abc.new(db_path, {'y': y_observed})"
    ]
   },
   {
@@ -205,7 +205,7 @@
     }
    ],
    "source": [
-    "print(\"ABC-SMC run ID:\", history.id)"
+    "print('ABC-SMC run ID:', history.id)"
    ]
   },
   {
@@ -270,7 +270,7 @@
     }
    ],
    "source": [
-    "history is abc.history"
+    "assert history is abc.history"
    ]
   },
   {
@@ -351,9 +351,9 @@
     }
    ],
    "source": [
-    "# Evaluate the model probabililties\n",
+    "# Evaluate the model probabilities\n",
     "model_probabilities = history.get_model_probabilities()\n",
-    "model_probabilities"
+    "print(model_probabilities)"
    ]
   },
   {

doc/examples/multiscale_agent_based.ipynb

@@ -118,7 +118,7 @@
     "    ecm_degradation_rate=8e-4,\n",
     "    ecm_division_threshold=1e-2,\n",
     ")\n",
-    "print(f\"Simulation took {time() - start_time:.2f}s\")"
+    "print(f'Simulation took {time() - start_time:.2f}s')"
    ]
   },
   {
@@ -157,29 +157,29 @@
     "fig.set_size_inches((16, 5))\n",
     "\n",
     "color = {\n",
-    "    \"growth_curve\": \"k\",\n",
-    "    \"extra_cellular_matrix_profile\": \"green\",\n",
-    "    \"proliferation_profile\": \"orange\",\n",
+    "    'growth_curve': 'k',\n",
+    "    'extra_cellular_matrix_profile': 'green',\n",
+    "    'proliferation_profile': 'orange',\n",
     "}\n",
     "\n",
     "x_label = {\n",
-    "    \"growth_curve\": \"Time (d)\",\n",
-    "    \"extra_cellular_matrix_profile\": \"Distance to rim (μm)\",\n",
-    "    \"proliferation_profile\": \"Distance to rim (μm)\",\n",
+    "    'growth_curve': 'Time (d)',\n",
+    "    'extra_cellular_matrix_profile': 'Distance to rim (μm)',\n",
+    "    'proliferation_profile': 'Distance to rim (μm)',\n",
     "}\n",
     "\n",
     "y_label = {\n",
-    "    \"growth_curve\": \"Radius (μm)\",\n",
-    "    \"extra_cellular_matrix_profile\": \"Extracellular matrix intensity\",\n",
-    "    \"proliferation_profile\": \"Fraction proliferating cells\",\n",
+    "    'growth_curve': 'Radius (μm)',\n",
+    "    'extra_cellular_matrix_profile': 'Extracellular matrix intensity',\n",
+    "    'proliferation_profile': 'Fraction proliferating cells',\n",
     "}\n",
     "\n",
     "for ax, (key, val) in zip(axes, observation.items()):\n",
     "    ax.plot(val, color=color[key])\n",
-    "    ax.set_title(capwords(key.replace(\"_\", \" \")))\n",
+    "    ax.set_title(capwords(key.replace('_', ' ')))\n",
     "    ax.set_xlabel(x_label[key])\n",
     "    ax.set_ylabel(y_label[key])\n",
-    "    if key.endswith(\"profile\"):\n",
+    "    if key.endswith('profile'):\n",
     "        ax.set_xlim(0, 600)"
    ]
   },
@@ -225,7 +225,7 @@
     ")\n",
     "\n",
     "prior = Distribution(\n",
-    "    **{key: RV(\"uniform\", a, b - a) for key, (a, b) in limits.items()}\n",
+    "    **{key: RV('uniform', a, b - a) for key, (a, b) in limits.items()}\n",
     ")"
    ]
   },
@@ -309,7 +309,7 @@
     }
    ],
    "source": [
-    "abc.new(\"sqlite:////tmp/test.db\", data_mean)"
+    "abc.new('sqlite:////tmp/test.db', data_mean)"
    ]
   },
   {
@@ -420,7 +420,7 @@
     "\n",
     "from pyabc import History\n",
     "\n",
-    "h_loaded = History(\"sqlite:///\" + stored_data_db)\n",
+    "h_loaded = History('sqlite:///' + stored_data_db)\n",
     "\n",
     "df, w = h_loaded.get_distribution(m=0, t=5)\n",
     "plot_kde_matrix(df, w, limits=limits);"
@@ -490,7 +490,7 @@
    ],
    "source": [
     "populations = h_loaded.get_all_populations()\n",
-    "(populations[populations.t >= 0].plot(\"t\", \"particles\", marker=\"o\"));"
+    "(populations[populations.t >= 0].plot('t', 'particles', marker='o'));"
    ]
   },
   {
@@ -516,7 +516,7 @@
     }
    ],
    "source": [
-    "print(f\"Execution time: {(time() - start_time)/60:.1f}m\")"
+    "print(f'Execution time: {(time() - start_time)/60:.1f}m')"
    ]
   },
   {

doc/examples/parameter_inference.ipynb

@@ -91,7 +91,7 @@
    "outputs": [],
    "source": [
     "def model(parameter):\n",
-    "    return {\"data\": parameter[\"mu\"] + 0.5 * np.random.randn()}"
+    "    return {'data': parameter['mu'] + 0.5 * np.random.randn()}"
    ]
   },
   {
@@ -109,7 +109,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "prior = pyabc.Distribution(mu=pyabc.RV(\"uniform\", 0, 5))"
+    "prior = pyabc.Distribution(mu=pyabc.RV('uniform', 0, 5))"
    ]
   },
   {
@@ -138,7 +138,7 @@
    "outputs": [],
    "source": [
     "def distance(x, x0):\n",
-    "    return abs(x[\"data\"] - x0[\"data\"])"
+    "    return abs(x['data'] - x0['data'])"
    ]
   },
   {
@@ -211,9 +211,9 @@
     }
    ],
    "source": [
-    "db_path = os.path.join(tempfile.gettempdir(), \"test.db\")\n",
+    "db_path = os.path.join(tempfile.gettempdir(), 'test.db')\n",
     "observation = 2.5\n",
-    "abc.new(\"sqlite:///\" + db_path, {\"data\": observation})"
+    "abc.new('sqlite:///' + db_path, {'data': observation})"
    ]
   },
   {
@@ -314,12 +314,12 @@
     "        w,\n",
     "        xmin=0,\n",
     "        xmax=5,\n",
-    "        x=\"mu\",\n",
-    "        xname=r\"$\\mu$\",\n",
+    "        x='mu',\n",
+    "        xname=r'$\\mu$',\n",
     "        ax=ax,\n",
-    "        label=f\"PDF t={t}\",\n",
+    "        label=f'PDF t={t}',\n",
     "    )\n",
-    "ax.axvline(observation, color=\"k\", linestyle=\"dashed\")\n",
+    "ax.axvline(observation, color='k', linestyle='dashed')\n",
     "ax.legend();"
    ]
   },