Merge branch 'develop' into eval_parameter_limits

.flake8

@@ -11,6 +11,8 @@ extend-ignore =
   E203
   # Don't be crazy if line too long
   E501
+  # Empty method in an abstract base class
+  B027
 
 per-file-ignores =
   # Imported but unused

.github/workflows/ci.yml

@@ -8,15 +8,15 @@ on:
   pull_request:
   schedule:
     # run Monday and Thursday at 03:18 UTC
-    - cron: '18 3 * * MON,THU'
+    - cron: '18 15 * * MON,THU'
 
 jobs:
 
   base:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10', '3.8']
+        python-version: ['3.11', '3.9']
 
     steps:
     - name: Check out repository
@@ -37,7 +37,7 @@ jobs:
       run: .github/workflows/install_deps.sh base R
 
     - name: Run tests
-      timeout-minutes: 12
+      timeout-minutes: 15
       run: tox -e base
 
     - name: Run visualization tests
@@ -54,7 +54,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10', '3.8']
+        python-version: ['3.11', '3.9']
 
     steps:
     - name: Check out repository
@@ -80,7 +80,7 @@ jobs:
       run: .github/workflows/install_deps.sh base R
 
     - name: Run tests
-      timeout-minutes: 10
+      timeout-minutes: 15
       run: tox -e external
 
     - name: Coverage
@@ -93,7 +93,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.11']
 
     steps:
     - name: Check out repository
@@ -114,7 +114,7 @@ jobs:
       run: .github/workflows/install_deps.sh amici
 
     - name: Run tests
-      timeout-minutes: 16
+      timeout-minutes: 20
       run: tox -e petab
 
     - name: Coverage
@@ -127,7 +127,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python-version: ['3.10', '3.8']
+        python-version: ['3.11', '3.9']
 
     steps:
       - name: Check out repository
@@ -148,7 +148,7 @@ jobs:
         run: .github/workflows/install_deps.sh
 
       - name: Run tests
-        timeout-minutes: 7
+        timeout-minutes: 10
         run: tox -e mac
 
       - name: Coverage
@@ -161,7 +161,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.11']
 
     steps:
     - name: Check out repository
@@ -182,14 +182,14 @@ jobs:
       run: .github/workflows/install_deps.sh
 
     - name: Run notebooks
-      timeout-minutes: 10
+      timeout-minutes: 15
       run: tox -e notebooks1
 
   notebooks2:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.11']
 
     steps:
     - name: Check out repository
@@ -210,14 +210,14 @@ jobs:
       run: .github/workflows/install_deps.sh R amici
 
     - name: Run notebooks
-      timeout-minutes: 10
+      timeout-minutes: 15
       run: tox -e notebooks2
 
   quality:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.11']
 
     steps:
     - name: Check out repository
@@ -240,11 +240,15 @@ jobs:
         pip install tox
 
     - name: Run quality checks
-      timeout-minutes: 10
-      run: tox -e project,flake8,doc
+      timeout-minutes: 5
+      run: tox -e project,flake8
+
+    - name: Build docs
+      timeout-minutes: 5
+      run: tox -e doc
 
     - name: Test migration
-      timeout-minutes: 3
+      timeout-minutes: 5
       run: tox -e migrate
 
     - name: Coverage

.gitignore

@@ -59,6 +59,7 @@ coverage.xml
 
 #documentation
 doc/_build
+doc/api
 
 # notebooks
 doc/examples/out

.pre-commit-config.yaml

@@ -11,12 +11,12 @@
 
 repos:
 - repo: https://github.com/psf/black
-  rev: 22.3.0
+  rev: 23.1.0
   hooks:
   - id: black
     description: The uncompromising code formatter
 - repo: https://github.com/pycqa/isort
-  rev: 5.10.1
+  rev: 5.12.0
   hooks:
   - id: isort
     name: isort (python)
@@ -27,14 +27,14 @@ repos:
     name: isort (pyi)
     types: [pyi]
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.2.3
+  rev: 1.6.1
   hooks:
     - id: nbqa-black
     - id: nbqa-pyupgrade
       args: [--py36-plus]
     - id: nbqa-isort
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.2.0
+  rev: v4.4.0
   hooks:
   - id: check-yaml
     description: Check yaml files for parseable syntax
@@ -55,6 +55,6 @@ repos:
   - id: style
     name: Check style
     description: Check style
-    entry: tox -e project,flake8
-    language: python
+    entry: tox -e flake8 --
+    language: system
     types: [python]

.readthedocs.yml

@@ -11,14 +11,13 @@ sphinx:
 
 # python requirements
 python:
-  version: 3.8
   install:
     - method: pip
       path: .
       extra_requirements:
         - doc
 
-# what to build
-formats:
-  - htmlzip
-  - pdf
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"

CHANGELOG.rst

@@ -8,6 +8,102 @@ Release Notes
 ...........
 
 
+0.12.12 (2023-08-18)
+--------------------
+
+Visualization:
+
+* Dash-based visualization server (#581)
+
+
+0.12.11 (2023-07-06)
+--------------------
+
+Fixes (#608):
+
+* Fix petab test suite (different name resolution)
+* Fix LocalTransition (pandas -> numpy argument)
+* Fix sklearn intersphinx
+
+
+0.12.10 (2023-05-09)
+--------------------
+
+General:
+
+* Update to Python 3.11, drop Python 3.8 support
+* Turn simple files into submodules for cleaner import
+* Fix dask sampler (change default pickling and use global function that it can pickle)
+
+Documentation:
+
+* Configure readthedocs build environment
+* Refactor API docs (add [+]; easier navigation)
+* Correct scipy intersphinx link
+* Add docstrings to submodules
+
+Minor fixes:
+
+* Flake8 fixes of dict creation from key+value
+* Fix imports from correct submodule in external submodule
+* Fix package versions in migration test
+
+Visualization:
+
+* Contour plots as a direct alternative to kernel density heat maps
+  and histograms (#597)
+* Fix column renaming in visserver
+
+
+0.12.9 (2023-03-01)
+-------------------
+
+Minor:
+
+* Improve documentation of p-norm (#592)
+* Update citation to JOSS
+* Temporarily fixate sqlalchemy version
+* Update pre-commit hooks (all #596)
+
+
+0.12.8 (2022-11-16)
+-------------------
+
+* Fix look-ahead implementation in case of biased proposals (#568)
+
+Minor:
+
+* Remove boteh in test env as distributed #7227 got fixed
+* Remove obsolete two gaussians test
+* Fix Mixin random seed (set it via /dev/urandom)
+* Update viserver to bokeh >= 3.0.1 (different import of TabPanel, Tabs)
+  (all #589)
+* Fix sqlalchemy warning "SAWarning: TypeDecorator BytesStorage()
+  will not produce a cache key" (#590)
+
+
+0.12.7 (2022-10-30)
+-------------------
+
+Minor:
+
+* Ignore B027 empty method in an abstract base class
+* Refactor EPSMixin
+* Fix EPSMixin for ConcurrentFutureSampler
+* Temporarily add bokeh to test due to dask error
+
+
+0.12.6 (2022-08-30)
+-------------------
+
+Minor:
+
+* Add JOSS paper of version 0.12.5
+* Update Julia reference DiffEqJump -> JumpProcesses (name change)
+* Unfix jinja2
+* Update flake8 dependencies after new issues
+
+
 0.12.5 (2022-06-21)
 -------------------
 

CITE.rst

@@ -5,21 +5,26 @@ When using pyABC version >= 0.8, please cite:
 
 * Schälte, Y., Klinger, E., Alamoudi, E., Hasenauer, J., 2022.
   pyABC: Efficient and robust easy-to-use approximate Bayesian computation.
-  arXiv.
-  https://doi.org/10.48550/arxiv.2203.13043.
+  Journal of Open Source Software.
+  https://doi.org/10.21105/joss.04304.
 
   .. code-block:: bibtex
 
-     @article{schaelte2022pyabc,
-       title = {pyABC: Efficient and robust easy-to-use approximate Bayesian computation},
-       author = {Schälte, Yannik and Klinger, Emmanuel and Alamoudi, Emad and Hasenauer, Jan},
-       journal = {arXiv},
-       year = {2022},
-       doi = {10.48550/arxiv.2203.13043},
-       url = {https://arxiv.org/abs/2203.13043},
-     }
-
-When using pyABC version < 0.8 or functionality not introduced in later versions, please cite:
+    @article{schaelte2022pyabc,
+      title = {pyABC: Efficient and robust easy-to-use approximate Bayesian computation},
+      author = {Schälte, Yannik and Klinger, Emmanuel and Alamoudi, Emad and Hasenauer, Jan},
+      journal = {Journal of Open Source Software},
+      publisher = {The Open Journal},
+      year = {2022},
+      volume = {7},
+      number = {74},
+      pages = {4304},
+      doi = {10.21105/joss.04304},
+      url = {https://doi.org/10.21105/joss.04304},
+    }
+
+When using pyABC version < 0.8 or functionality not introduced in later
+versions, please (also) cite:
 
 * Klinger, E., Rickert, D., Hasenauer, J., 2018.
   pyABC: distributed, likelihood-free inference.