Release v0.5.2

Merge pull request #1406 from ICB-DCM/develop
ICB-DCM · May 31, 2024 · d38005e · d38005e
2 parents d8333bd + c966568
commit d38005e
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.11']
+        python-version: ['3.10', '3.12']
 
     steps:
     - name: Check out repository
@@ -41,7 +41,7 @@ jobs:
         path: |
           ~/.cache/pip
           .tox/
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
+        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh amici
@@ -60,10 +60,10 @@ jobs:
         file: ./coverage.xml
 
   mac:
-    runs-on: macos-latest
+    runs-on: macos-13  # TODO: change to macos-latest after the next release
     strategy:
       matrix:
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - name: Check out repository
@@ -80,14 +80,14 @@ jobs:
         path: |
           ~/.cache/pip
           .tox/
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci
+        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh amici
 
     - name: Run tests
       timeout-minutes: 30
-      run: tox -e base
+      run: ulimit -n 65536 65536 && tox -e base
 
     - name: Coverage
       uses: codecov/codecov-action@v3
@@ -99,7 +99,7 @@ jobs:
     runs-on: windows-latest
     strategy:
       matrix:
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - name: Check out repository
@@ -116,7 +116,7 @@ jobs:
         path: |
           ~\AppData\Local\pip\Cache
           .tox
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci
+        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"
 
     - name: Install dependencies
       run: |
@@ -132,7 +132,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.11']
+        python-version: ['3.10', '3.12']
 
     steps:
     - name: Check out repository
@@ -149,7 +149,7 @@ jobs:
         path: |
           ~/.cache/pip
           .tox/
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
+        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh amici pysb
@@ -171,7 +171,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.11']
+        python-version: ['3.10', '3.12']
 
     # needed to allow julia-actions/cache to delete old caches that it has created
     permissions:
@@ -193,7 +193,7 @@ jobs:
         path: |
           ~/.cache/pip
           .tox/
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
+        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"
 
     - name: Install julia
       uses: julia-actions/setup-julia@v1
@@ -225,8 +225,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        # ipopt does not work on 3.9 (https://github.com/mechmotum/cyipopt/issues/225)
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - name: Check out repository
@@ -243,7 +242,7 @@ jobs:
         path: |
           ~/.cache/pip
           .tox/
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
+        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh ipopt
@@ -262,7 +261,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.11']
+        python-version: ['3.10', '3.12']
 
     steps:
     - name: Check out repository
@@ -279,7 +278,7 @@ jobs:
         path: |
           ~/.cache/pip
           .tox/
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
+        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh amici
@@ -298,7 +297,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.11']
+        python-version: ['3.10', '3.12']
 
     steps:
     - name: Check out repository
@@ -315,7 +314,7 @@ jobs:
         path: |
           ~/.cache/pip
           .tox/
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
+        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh amici
@@ -334,7 +333,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11']
+        python-version: ['3.12']
 
     steps:
     - name: Check out repository
@@ -351,7 +350,7 @@ jobs:
         path: |
           ~/.cache/pip
           .tox/
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
+        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"
 
     - name: Install dependencies
       run: pip install tox pre-commit
@@ -383,7 +382,7 @@ jobs:
         path: |
           ~/.cache/pip
           .tox/
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
+        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh doc amici
@@ -399,7 +398,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
 
     steps:
     - name: Check out repository
@@ -416,7 +415,7 @@ jobs:
         path: |
           ~/.cache/pip
           .tox/
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
+        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh amici ipopt
@@ -429,7 +428,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
 
     steps:
     - name: Check out repository
@@ -446,7 +445,7 @@ jobs:
         path: |
           ~/.cache/pip
           .tox/
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
+        key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh amici

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.12']
 
     steps:
     - name: Check out repository

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -6,6 +6,37 @@ Release notes
 ..........
 
 
+0.5.2 (2024-05-27)
+-------------------
+
+* **New Feature**: Variational inference with PyMC (#1306)
+* PEtab
+    * Import of petab independent of amici (#1355)
+* Problem
+    * Added option to sample startpoints for a problem, from the problem directly. (#1364)
+    * More detailed defaults for problem.get_full_vector (#1393)
+    * Save pypesto and python version to the problem. (#1382)
+* Objective
+    * Fix calling priors in sampling with fixed parameters (#1378)
+    * Fix JaxObjective (#1400)
+* Optimize
+    * ESS optimizers: suppress divide-by-zero warnings; report n_eval (#1380)
+    * SacessOptimizer: collect worker stats (#1381)
+    * Add load method to Hdf5AmiciHistory (#1370)
+* Hierarchical
+    * Relative: fix log of zero for default 0 sigma values (#1377)
+* Sample
+    * Fix pypesto.sample.geweke_test.spectrum for nfft<=3 (#1388)
+* Visualize
+    * Handle correlation plot with nans (#1365)
+* General
+    * Remove scipy requirement from pypesto[pymc] (#1376)
+    * Require and test python >=3.10 according to NEP 29 (#1379)
+    * Fix various warnings (#1384)
+    * Small changes to GHA actions and tests (#1386, #1387, #1402, #1385)
+    * Improve Documentation (#1394, #1391, #1399, #1292, #1390)
+
+
 0.5.0 (2024-04-10)
 -------------------
 

diff --git a/README.md b/README.md
@@ -25,12 +25,15 @@ pyPESTO features include:
 * Parameter estimation pipeline for systems biology problems specified in
   [SBML](http://sbml.org/) and [PEtab](https://github.com/PEtab-dev/PEtab)
   ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/petab_import.ipynb))
+* Parameter estimation with relative (scaled and offset) data as described in
+  [Schmiester et al. (2020)](https://doi.org/10.1093/bioinformatics/btz581).
+  ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/relative_data.ipynb))
 * Parameter estimation with ordinal data as described in
   [Schmiester et al. (2020)](https://doi.org/10.1007/s00285-020-01522-w) and
   [Schmiester et al. (2021)](https://doi.org/10.1093/bioinformatics/btab512).
-  ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/ordinal.ipynb))
-* Parameter estimation with censored data. ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/censored.ipynb))
-* Parameter estimation with nonlinear-monotone data. ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/nonlinear_monotone.ipynb))
+  ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/ordinal_data.ipynb))
+* Parameter estimation with censored data. ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/censored_data.ipynb))
+* Parameter estimation with nonlinear-monotone data. ([example](https://github.com/ICB-DCM/pyPESTO/blob/master/doc/example/semiquantitative_data.ipynb))
 
 ## Quick install
 

diff --git a/doc/example/amici.ipynb b/doc/example/amici.ipynb
@@ -36,7 +36,6 @@
    "source": [
     "# import\n",
     "import logging\n",
-    "import random\n",
     "import tempfile\n",
     "from pprint import pprint\n",
     "\n",
@@ -57,7 +56,8 @@
     "mpl.rcParams[\"figure.dpi\"] = 100\n",
     "mpl.rcParams[\"font.size\"] = 18\n",
     "\n",
-    "random.seed(1912)\n",
+    "# Set seed for reproducibility\n",
+    "np.random.seed(1912)\n",
     "\n",
     "\n",
     "# name of the model that will also be the name of the python module\n",
@@ -929,8 +929,6 @@
    "outputs": [],
    "source": [
     "%%time\n",
-    "# Set seed for reproducibility\n",
-    "np.random.seed(1)\n",
     "result = optimize.minimize(\n",
     "    problem=problem,\n",
     "    optimizer=optimizer,\n",