Build: Drop support for Python 3.8

.auto-changelog

@@ -4,7 +4,7 @@
     "tagPrefix": "synthesis-workflow-v",
     "commitLimit": false,
     "backfillLimit": false,
-    "ignoreCommitPattern": "^Release:? [0-9]+\\.[0-9]+\\.[0-9]+$|^Update CHANGELOG.*|.*\\[skip-changelog\\].*|^\\[pre-commit.ci\\]|^\\(dependabot\\) .*",
+    "ignoreCommitPattern": "^Release:? [0-9]+\\.[0-9]+\\.[0-9]+( ?\\(#[0-9]+\\))?$|^Update CHANGELOG.*|.*\\[skip-changelog\\].*|^\\[pre-commit.ci\\]|^\\(dependabot\\) .*",
     "commitUrl": "https://bbpgitlab.epfl.ch/neuromath/synthesis-workflow/commit/{id}",
     "issueUrl": "https://bbpgitlab.epfl.ch/neuromath/synthesis-workflow/issues/{id}",
     "mergeUrl": "https://bbpgitlab.epfl.ch/neuromath/synthesis-workflow/merge_requests/{id}",

.auto-changelog-template.hbs

@@ -136,7 +136,7 @@ Example Definitions
         - {{message}} ({{author}}{{#if href}} - [#{{id}}]({{href}}){{/if}})
       {{/commit-list}}
 
-      {{#commit-list merges heading='### General Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[bB]uild:|^[bB]uild\(|^[dD]eprecate:|^[dD]eprecate\(|^[fF]eat:|^[fF]eat\(|^[fF]ix:|^[fF]ix\(|^[cC]hore:|^[cC]hore\(|^[cC][iI]:|^[cC][iI]\(|^[dD]ocs:|^[dD]ocs\(|^[rR]efactor:|^[rR]efactor\(|^[tT]est:|^[tT]est\(|^[sS]tyle:|^[sS]tyle\(|^[pP]erf:|^[pP]erf\(|\[skip-changelog\]'}}
+      {{#commit-list merges heading='### General Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[bB]uild:|^[bB]uild ?\(|^[dD]eprecate:|^[dD]eprecate ?\(|^[fF]eat:|^[fF]eat ?\(|^[fF]ix:|^[fF]ix ?\(|^[cC]hore:|^[cC]hore ?\(|^[cC][iI]:|^[cC][iI] ?\(|^[dD]ocs:|^[dD]ocs ?\(|^[rR]efactor:|^[rR]efactor ?\(|^[tT]est:|^[tT]est ?\(|^[sS]tyle:|^[sS]tyle ?\(|^[pP]erf:|^[pP]erf ?\(|\[skip-changelog\]'}}
         - {{message}} ({{author}}{{#if href}} - [#{{id}}]({{href}}){{/if}})
       {{/commit-list}}
 
@@ -190,7 +190,7 @@ Example Definitions
         - {{subject}} ({{author}}{{#if href}} - [{{shorthash}}]({{href}}){{/if}})
       {{/commit-list}}
 
-      {{#commit-list commits heading='### General Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[bB]uild:|^[bB]uild\(|^[dD]eprecate:|^[dD]eprecate\(|^[fF]eat:|^[fF]eat\(|^[fF]ix:|^[fF]ix\(|^[cC]hore:|^[cC]hore\(|^[cC][iI]:|^[cC][iI]\(|^[dD]ocs:|^[dD]ocs\(|^[rR]efactor:|^[rR]efactor\(|^[tT]est:|^[tT]est\(|^[sS]tyle:|^[sS]tyle\(|^[pP]erf:|^[pP]erf\(|\[skip-changelog\]'}}
+      {{#commit-list commits heading='### General Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[bB]uild:|^[bB]uild ?\(|^[dD]eprecate:|^[dD]eprecate ?\(|^[fF]eat:|^[fF]eat ?\(|^[fF]ix:|^[fF]ix ?\(|^[cC]hore:|^[cC]hore ?\(|^[cC][iI]:|^[cC][iI] ?\(|^[dD]ocs:|^[dD]ocs ?\(|^[rR]efactor:|^[rR]efactor ?\(|^[tT]est:|^[tT]est ?\(|^[sS]tyle:|^[sS]tyle ?\(|^[pP]erf:|^[pP]erf ?\(|\[skip-changelog\]'}}
         - {{subject}} ({{author}}{{#if href}} - [{{shorthash}}]({{href}}){{/if}})
       {{/commit-list}}
 

.copier-answers.yml

@@ -1,6 +1,6 @@
 # Changes here will be overwritten by Copier
 
-_commit: 0.1.52
+_commit: 0.1.59
 _src_path: git@bbpgitlab.epfl.ch:neuromath/python-template.git
 author_email: bbp-ou-cells@groupes.epfl.ch
 author_name: bbp-ou-cells
@@ -9,7 +9,7 @@ copyright_year: '2022'
 distribution_name: synthesis-workflow
 download_url: https://bbpgitlab.epfl.ch/neuromath/synthesis-workflow
 init_git: false
-maintainer: null
+maintainer: ''
 package_name: synthesis_workflow
 project_description: Workflow used for synthesis and its validation.
 project_name: Synthesis Workflow

.gitlab-ci.yml

@@ -15,9 +15,10 @@ include:
         - /ci/jobs/auto-release.yml
         - /ci/jobs/check-merge-request-title.yml
         - /ci/lib/pytest-template.yml
-        - /ci/jobs/py38.yml
         - /ci/jobs/py39.yml
         - /ci/jobs/py310.yml
+        - /ci/jobs/py311.yml
+        - /ci/jobs/py312.yml
         - /ci/jobs/min_versions.yml
         - /ci/jobs/coverage.yml
 

pyproject.toml

@@ -8,10 +8,10 @@ build-backend = "setuptools.build_meta"
 [tool.black]
 line-length = 100
 target-version = [
-    "py38",
     "py39",
     "py310",
     "py311",
+    "py312",
 ]
 
 [tool.pydocstyle]

requirements/base.pip

@@ -3,7 +3,7 @@ bluepy>=2.5,<3
 bluepy-configfile>=0.1.19
 bluepymm>=0.8.5
 bluepyparallel>=0.0.8
-brainbuilder>=0.19
+brainbuilder>=0.20
 diameter_synthesis>=0.5.4
 dictdiffer>=0.9
 gitpython>=3.1.30
@@ -15,11 +15,11 @@ luigi-tools>=0.2.1
 matplotlib>=3.6.2
 morph_tool>=2.9.1,<3
 morphio>=3.3.6,<4
-neuroc>=0.2.8,<1
+neuroc>=0.3.0,<1
 neurocollage>=0.3.3
 neurom>=3.2.2,<4
 neurots>=3.6,<4
-numpy>=1.24.1
+numpy>=1.26.4
 pandas>=1.5.3
 placement_algorithm>=2.3.1
 PyYAML>=6

requirements/test.pip

@@ -9,6 +9,5 @@ pytest-html>=3
 pytest-xdist>=3.0.2
 
 # Pin versions for tests
-numpy==1.24.*
 matplotlib==3.6.*
 seaborn==0.12.*

setup.py

@@ -40,7 +40,7 @@
     license="BBP-internal-confidential",
     packages=find_namespace_packages("src"),
     package_dir={"": "src"},
-    python_requires=">=3.8",
+    python_requires=">=3.9",
     version=VERSION,
     install_requires=reqs,
     extras_require={
@@ -60,10 +60,10 @@
         "Intended Audience :: Science/Research",
         "Programming Language :: Python",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
 )

tox.ini

@@ -10,7 +10,7 @@ envlist =
     lint
     docs
     min_versions
-    py{38,39,310,311}
+    py{39,310,311,312}
     coverage
 
 minversion = 3.18
@@ -71,10 +71,10 @@ commands =
     twine check {envtmpdir}/dist/*
 
 [testenv:min_versions]
-basepython = python3.8
+basepython = python3.9
 
 [testenv:lint]
-basepython = python3.8
+basepython = python3.9
 deps =
     pre-commit
     pylint
@@ -83,7 +83,7 @@ commands =
     pylint -j {env:PYLINT_NPROCS:1} {[base]files}
 
 [testenv:format]
-basepython = python3
+basepython = python3.9
 skip_install = true
 deps =
     codespell