Fix: Fix OS (#1)

* remove dev

* remove placement-algo dep

* Chore: Bump Copier template

* Fix: Lint and doc

* fix dep

* Test: Check diff-pdf-visually outputs

* Fix: Lint

---------

Co-authored-by: Adrien Berchet <[email protected]>

.codespellrc

@@ -1,2 +1,3 @@
 [codespell]
-skip = .git/*
+skip = .git/*,*.pdf
+ignore-words-list = INH

.copier-answers.yml

@@ -1,6 +1,6 @@
 # Changes here will be overwritten by Copier
 
-_commit: 0.1.65
+_commit: 0.1.67
 _src_path: [email protected]:neuromath/python-template.git
 author_email: ''
 author_name: Blue Brain Project, EPFL
@@ -9,11 +9,11 @@ copyright_year: '2022'
 distribution_name: synthesis-workflow
 download_url: https://github.com/BlueBrain/synthesis-workflow
 init_git: false
-maintainer: Adrien Berchet
+maintainer: Adrien Berchet (@adrien-berchet)
 package_name: synthesis_workflow
 project_description: Workflow used for synthesis and its validation.
 project_name: Synthesis Workflow
-project_url: https://synthesis_workflow.readthedocs.io
+project_url: https://synthesis-workflow.readthedocs.io
 repository_name: synthesis-workflow
 repository_namespace: BlueBrain
 repository_provider: github

.github/ISSUE_TEMPLATE/bug_report.yaml

@@ -43,7 +43,7 @@ Your reports must include the following features:
   - type: input
     id: relevant_documentation
     attributes:
-      label: Optional link from https://synthesis_workflow.readthedocs.io which documents the behavior that is expected
+      label: Optional link from https://synthesis-workflow.readthedocs.io which documents the behavior that is expected
       description: "
 Please make sure the behavior you are seeing is definitely in contradiction to what's documented as the correct behavior.
 "

.github/ISSUE_TEMPLATE/feature_request.yaml

@@ -12,7 +12,7 @@ body:
 Thanks for taking the time to fill out this feature request!
 
 
-Before submitting, make sure the feature does not already exist in the [documentation](https://synthesis_workflow.readthedocs.io) and that you searched in the [issue list](https://github.com/BlueBrain/synthesis-workflow/issues) that a similar feature request has not already been reported.
+Before submitting, make sure the feature does not already exist in the [documentation](https://synthesis-workflow.readthedocs.io) and that you searched in the [issue list](https://github.com/BlueBrain/synthesis-workflow/issues) that a similar feature request has not already been reported.
 If it is not the case, please read the following guidelines.
 
 ### GUIDELINES FOR REQUESTING HELP

.github/ISSUE_TEMPLATE/how_to_use.yaml

@@ -12,7 +12,7 @@ body:
 Thanks for using this package and taking the time to fill out this help request!
 
 
-Before submitting, make sure you read the [documentation](https://synthesis_workflow.readthedocs.io) carefully.
+Before submitting, make sure you read the [documentation](https://synthesis-workflow.readthedocs.io) carefully.
 If you still have a question, you should search in the [issue list](https://github.com/BlueBrain/synthesis-workflow/issues) that a similar issue has not already been reported, you might find your answer there.
 If it is not the case, please read the following guidelines.
 

.github/workflows/run-tox.yml

@@ -34,7 +34,7 @@ jobs:
       # This action should only be used when you need extra system packages
       uses: awalsh128/cache-apt-pkgs-action@latest
       with:
-        packages: graphviz
+        packages: graphviz poppler-utils
         version: 1.0
         execute_install_scripts: true
     - name: Cache tox and precommit environments

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -11,7 +11,7 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook
-    rev: v9.17.0
+    rev: v9.18.0
     hooks:
         - id: commitlint
           stages:
@@ -22,7 +22,7 @@ repos:
     hooks:
       - id: isort
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
   - repo: https://github.com/codespell-project/codespell

.pylintrc

@@ -51,6 +51,4 @@ ignore-docstrings=yes
 [TYPECHECK]
 # List of classes names for which member attributes should not be checked
 # (useful for classes with attributes dynamically set).
-
-# as of numpy 1.8.0, name resolution seems to be a problem. Ignore lookups in numpy
-# ignored-classes=numpy,list
+extension-pkg-allow-list=lxml.etree

AUTHORS.md

@@ -1,5 +1,5 @@
 # Maintainer
 
-Adrien Berchet
+Adrien Berchet (@adrien-berchet)
 
 # Contributors

CONTRIBUTING.md

@@ -59,7 +59,7 @@ When you wish to contribute to the code base, please consider the following guid
   or
 
   ```shell
-  tox -e py39 -e lint -e docs -e check-packaging
+  tox run -e py39,lint,docs,check-packaging
   ```
 
 * Commit your changes using a descriptive commit message.

docs/Makefile

@@ -21,4 +21,4 @@ help:
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
 clean:
-	@rm -rf $(BUILDDIR) $(SOURCEDIR)/examples $(SOURCEDIR)/generated
+	@rm -rf $(BUILDDIR) $(SOURCEDIR)/examples $(SOURCEDIR)/autoapi

docs/source/conf.py

@@ -25,10 +25,11 @@
 
 # -- Project information -----------------------------------------------------
 
-project = "Synthesis Workflow"
+project_name = "Synthesis Workflow"
+package_name = "synthesis-workflow"
 
 # The short X.Y version
-version = metadata.version("synthesis-workflow")
+version = metadata.version(package_name)
 
 # The full version, including alpha/beta/rc tags
 release = version
@@ -94,10 +95,10 @@
 # html_static_path = ['_static']
 
 html_theme_options = {
-    "metadata_distribution": "synthesis-workflow",
+    "metadata_distribution": package_name,
 }
 
-html_title = project
+html_title = project_name
 
 # If true, links to the reST sources are added to the pages.
 html_show_sourcelink = False

docs/source/contributing.rst

@@ -0,0 +1 @@
+.. mdinclude:: ../../CONTRIBUTING.md

docs/source/index.rst

@@ -50,3 +50,4 @@ The :doc:`./api_ref` page contains detailed documentation of:
    cli
    api_ref
    changelog
+   contributing

docs/source/synthesis_methodology.rst

@@ -100,6 +100,6 @@ Here is an example of such ``context_constraints`` entry:
 
 More details on the models can be found here:
 
-* `TNS <https://bbpteam.epfl.ch/documentation/projects/TNS/latest/index.html>`_
-* <region-grower doc URL> (does not exist yet)
-* <placement-algorithm.app.synthesis doc URL> (does not exist yet)
+* `NeuroTS <https://neurots.readthedocs.io/en/stable>`_
+* `region-grower <https://region-grower.readthedocs.io/en/stable/>`_
+* `placement-algorithm <https://github.com/BlueBrain/placement-algorithm>`_

requirements/base.pip

@@ -1,9 +1,5 @@
-atlas_analysis>=0.0.5
-bluepy>=2.5,<3
-bluepy-configfile>=0.1.19
-bluepymm>=0.8.5
 bluepyparallel>=0.0.8
-brainbuilder>=0.20
+brainbuilder>=0.20.1
 diameter_synthesis>=0.5.4
 dictdiffer>=0.9
 gitpython>=3.1.30
@@ -16,16 +12,15 @@ matplotlib>=3.6.2
 morph_tool>=2.9.1,<3
 morphio>=3.3.6,<4
 neuroc>=0.3.0,<1
-neurocollage>=0.3.3
+neurocollage>=0.3.6
 neurom>=3.2.2,<4
 neurots>=3.6,<4
 numpy>=1.26.4
-pandas>=1.5.3
-placement_algorithm>=2.3.1
+pandas>=2.1
 PyYAML>=6
-region_grower>=1.3,<2
-scipy>=1.10
+region_grower>=1.5.1,<2
+scipy>=1.13
 seaborn>=0.12.2
 tmd>=2.3
 tqdm>=4.64.1
-voxcell>=3.1.3,<4
+voxcell>=3.1.5,<4

setup.py

@@ -1,19 +1,10 @@
 """Setup for the synthesis-workflow package."""
 
-import importlib
 from pathlib import Path
 
 from setuptools import find_namespace_packages
 from setuptools import setup
 
-spec = importlib.util.spec_from_file_location(
-    "src.version",
-    "src/version.py",
-)
-module = importlib.util.module_from_spec(spec)
-spec.loader.exec_module(module)
-VERSION = module.VERSION
-
 # Read the requirements
 with open("requirements/base.pip", "r", encoding="utf-8") as f:
     reqs = f.read().splitlines()
@@ -28,21 +19,23 @@
 
 setup(
     name="synthesis-workflow",
-    author="bbp-ou-cells",
-    author_email="[email protected]",
+    author="Blue Brain Project, EPFL",
     description="Workflow used for synthesis and its validation.",
     long_description=Path("README.rst").read_text(encoding="utf-8"),
     long_description_content_type="text/x-rst",
-    url="https://bbpteam.epfl.ch/documentation/projects/synthesis-workflow",
+    url="https://synthesis-workflow.readthedocs.io",
     project_urls={
-        "Tracker": "https://bbpteam.epfl.ch/project/issues/projects/CELLS/issues",
-        "Source": "https://bbpgitlab.epfl.ch/neuromath/synthesis-workflow",
+        "Tracker": "https://github.com/BlueBrain/synthesis-workflow/issues",
+        "Source": "https://github.com/BlueBrain/synthesis-workflow",
     },
-    license="BBP-internal-confidential",
+    license="Apache License 2.0",
     packages=find_namespace_packages("src"),
     package_dir={"": "src"},
     python_requires=">=3.9",
-    version=VERSION,
+    use_scm_version=True,
+    setup_requires=[
+        "setuptools_scm",
+    ],
     install_requires=reqs,
     extras_require={
         "docs": doc_reqs,
@@ -56,6 +49,7 @@
     },
     include_package_data=True,
     classifiers=[
+        # TODO: Update to relevant classifiers
         "Development Status :: 2 - Pre-Alpha",
         "Intended Audience :: Education",
         "Intended Audience :: Science/Research",