Merge pull request #598 from ICB-DCM/develop

* Contour plots as a direct alternative to kernel density heat maps (#597) * add contour plot * add test * fix C416 unnecessary dict comprehension * Various fixes (#604) * fix C416 unnecessary dict comprehension * bump rtd python version * update migration test * fix .rtd file * ensure jquery installed for [+] in docs * ignore warnings * refactor api docs * fix typo * update to py3.11 * fox * extend migration time * fix dask by global function; fix sqlalchemy update * update migrate test with fixed versions * fix visserver weird wrong rename * update changelog
ICB-DCM · May 9, 2023 · 5508549 · 5508549
2 parents 7d9c109 + 99c0b86
commit 5508549
Show file tree

Hide file tree

Showing 76 changed files with 850 additions and 315 deletions.
diff --git a/.github/workflows/ci.yml b/.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
@@ -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
@@ -93,7 +93,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.11']
 
     steps:
     - name: Check out repository
@@ -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
@@ -161,7 +161,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.11']
 
     steps:
     - name: Check out repository
@@ -189,7 +189,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.11']
 
     steps:
     - name: Check out repository
@@ -217,7 +217,7 @@ jobs:
     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

diff --git a/.gitignore b/.gitignore
@@ -59,6 +59,7 @@ coverage.xml
 
 #documentation
 doc/_build
+doc/api
 
 # notebooks
 doc/examples/out

diff --git a/.readthedocs.yml b/.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"
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -7,6 +7,36 @@ Release Notes
 0.12 Series
 ...........
 
+
+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)
 -------------------
 
@@ -17,6 +47,7 @@ Minor:
 * Temporarily fixate sqlalchemy version
 * Update pre-commit hooks (all #596)
 
+
 0.12.8 (2022-11-16)
 -------------------
 
@@ -43,6 +74,7 @@ Minor:
 * Fix EPSMixin for ConcurrentFutureSampler
 * Temporarily add bokeh to test due to dask error
 
+
 0.12.6 (2022-08-30)
 -------------------
 

diff --git a/doc/api.rst b/doc/api.rst
@@ -1,29 +1,33 @@
 API reference
 =============
 
+.. autosummary::
+   :toctree: api
 
-.. automodule:: pyabc
-
-.. toctree::
-   :maxdepth: 3
-
-   api_inference
-   api_distance
-   api_acceptor
-   api_model
-   api_epsilon
-   api_predictor
-   api_sumstat
-   api_datastore
-   api_transition
-   api_populationstrategy
-   api_sampler
-   api_parameters
-   api_population
-   api_random_variables
-   api_sge
-   api_external
-   api_petab
-   api_copasi
-   api_visualization
-   api_weightedstatistics
+   pyabc.acceptor
+   pyabc.copasi
+   pyabc.distance
+   pyabc.epsilon
+   pyabc.external
+   pyabc.external.r
+   pyabc.external.julia
+   pyabc.inference
+   pyabc.inference_util
+   pyabc.model
+   pyabc.parameters
+   pyabc.petab
+   pyabc.population
+   pyabc.populationstrategy
+   pyabc.predictor
+   pyabc.random_choice
+   pyabc.random_variables
+   pyabc.sampler
+   pyabc.settings
+   pyabc.sge
+   pyabc.storage
+   pyabc.sumstat
+   pyabc.transition
+   pyabc.util
+   pyabc.visserver
+   pyabc.visualization
+   pyabc.weighted_statistics
diff --git a/doc/api_acceptor.rst b/doc/api_acceptor.rst
diff --git a/doc/api_copasi.rst b/doc/api_copasi.rst
diff --git a/doc/api_datastore.rst b/doc/api_datastore.rst
diff --git a/doc/api_distance.rst b/doc/api_distance.rst
diff --git a/doc/api_epsilon.rst b/doc/api_epsilon.rst
diff --git a/doc/api_external.rst b/doc/api_external.rst
diff --git a/doc/api_inference.rst b/doc/api_inference.rst
diff --git a/doc/api_model.rst b/doc/api_model.rst
diff --git a/doc/api_parameters.rst b/doc/api_parameters.rst
diff --git a/doc/api_petab.rst b/doc/api_petab.rst
diff --git a/doc/api_population.rst b/doc/api_population.rst
diff --git a/doc/api_populationstrategy.rst b/doc/api_populationstrategy.rst
diff --git a/doc/api_predictor.rst b/doc/api_predictor.rst
diff --git a/doc/api_random_variables.rst b/doc/api_random_variables.rst
diff --git a/doc/api_sampler.rst b/doc/api_sampler.rst
diff --git a/doc/api_sge.rst b/doc/api_sge.rst
diff --git a/doc/api_sumstat.rst b/doc/api_sumstat.rst
diff --git a/doc/api_transition.rst b/doc/api_transition.rst
diff --git a/doc/api_visualization.rst b/doc/api_visualization.rst
diff --git a/doc/api_weightedstatistics.rst b/doc/api_weightedstatistics.rst
diff --git a/doc/conf.py b/doc/conf.py
@@ -49,6 +49,8 @@
     'nbsphinx',
     # code highlighting in jupyter cells
     'IPython.sphinxext.ipython_console_highlighting',
+    # ensure that jQuery is installed
+    'sphinxcontrib.jquery',
 ]
 
 # default autodoc options
@@ -57,13 +59,15 @@
     'members': True,
     'special-members': '__init__, __call__',
     'show-inheritance': True,
+    'autodoc_inherit_docstrings': True,
+    'imported-members': True,
 }
 
 # links for intersphinx
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3', None),
     'numpy': ('https://numpy.org/devdocs/', None),
-    'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/', None),
     'pandas': ('https://pandas.pydata.org/pandas-docs/dev', None),
     'petab': ('https://petab.readthedocs.io/en/stable/', None),
     'amici': ('https://amici.readthedocs.io/en/latest/', None),