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

Author: yannikschaelte

.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

.gitignore

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

.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

@@ -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)
 -------------------
 

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