.git-blame-ignore-revs

+# This file contains revisions to be ignored by git blame.
+# These revisions are expected to be formatting-only changes.
+#
+# Calling `git blame --ignore-revs-file .git-blame-ignore-revs` will
+# tell git blame to ignore changes made by these revisions when assigning
+# assigning blame, as if the change never happened.
+#
+# You can enable this as a default for your local repository by running
+# `git config blame.ignoreRevsFile .git-blame-ignore-revs`
+# This will probably be automatically picked by your IDE
+# (VSCode+GitLens and JetBrains products are confirmed to this)
+#
+# Important: if you are switching to the branch without this file,
+# `git blame` will fail with an error
+#
+# Guidelines:
+# - Only large automated refactorings are expected to be included in this file.
+#   Do not add new revision just because it feels unimportant
+# - When adding sinle revision use inline comment to link relevant issue/MR
+#   Example:
+##   d4a8b7307acc2dc8a8833ccfa65426ad28b3ffc9 # https://gitlab.teklia.com/atr/dan/issues/12345
+# - When adding multiple revisions precede each addition (this could be multiple revisions) with a link to
+#   line with word START and link to relevant issue/MR and conclude with line END and link to the
+#   same issue/MR
+#   Example:
+#   # START https://gitlab.teklia.com/atr/dan/issues/12345
+#   6f0bd2d8a1e6cd2e794cd39976e9756e0c85ac66
+#   d53974df11dbc22cbea9dc7dcbc9896c25979a27
+#   ... <rest of the list>
+#   # END https://gitlab.teklia.com/atr/dan/issues/12345
+# - Please append new lines to the end of the file, no matter of real chronological
+#   order of revisions
+# - Since this is using hashes for reformatting it might be a good idea to update
+#   this file in separate MR when relevant changes already landed in master. By
+#   utilizing this manner you will be safe from random rebase/squash issues
+# - Only put full 40-character hashes on this list
+
+# START https://gitlab.teklia.com/atr/dan/-/merge_requests/408
+05db961d87448647e8f59f6b728b321b17263042
+838c7df40b3c6ba223008416e2a654fe40bfcf4a
+# END https://gitlab.teklia.com/atr/dan/-/merge_requests/408

.gitlab-ci.yml

@@ -42,19 +42,11 @@ test:
     - apt-get update -q
     - apt-get install -q -y libgl1
 
-    # Add netrc file
-    - |
-      echo "
-      machine gitlab.teklia.com
-      login gitlab-ci-token
-      password $CI_JOB_TOKEN
-      " > ~/.netrc
-
   except:
     - schedules
 
   script:
-    - tox -- -v
+    - tox -e teklia-dan -- -v
 
 docker-build:
   stage: build
@@ -68,15 +60,6 @@ docker-build:
   except:
     - schedules
 
-  before_script:
-    # Add netrc file
-    - |
-      echo "
-      machine gitlab.teklia.com
-      login gitlab-ci-token
-      password $CI_JOB_TOKEN
-      " > ~/.netrc
-
   script:
     - ci/build.sh
 
@@ -88,18 +71,10 @@ docker-build:
       - public
 
   before_script:
-    # Add netrc file
-    - |
-      echo "
-      machine gitlab.teklia.com
-      login gitlab-ci-token
-      password $CI_JOB_TOKEN
-      " > ~/.netrc
-
-    - pip install --index-url https://gitlab.teklia.com/api/v4/projects/210/packages/pypi/simple -e .[docs]
+    - pip install tox
 
   script:
-    - mkdocs build --strict --verbose
+    - tox -e doc
 
 docs-build:
   extends: .docs
@@ -177,30 +152,22 @@ deploy-pypi:
   only:
     - tags
 
-  variables:
-    TWINE_USERNAME: gitlab-ci-token
-    TWINE_PASSWORD: ${CI_JOB_TOKEN}
-    TWINE_REPOSITORY_URL: ${CI_API_V4_URL}/projects/${CI_PROJECT_ID}/packages/pypi
-
   before_script:
-    - pip install twine
+    - pip install twine build
 
   script:
-    - python setup.py sdist bdist_wheel
-    - twine upload --repository-url ${TWINE_REPOSITORY_URL} dist/*
+    - python -m build
+    - twine upload -r pypi dist/*
 
 bump-python-deps:
   stage: deploy
   image: registry.gitlab.teklia.com/infra/devops:latest
 
-  variables:
-    PYPI_GITLAB_URL: https://gitlab.teklia.com/api/v4/projects/210/packages
-
   only:
     - schedules
 
   script:
-    - devops python-deps requirements.txt doc-requirements.txt
+    - devops python-deps pyproject.toml doc-requirements.txt
 
 release-notes:
   stage: deploy

.pre-commit-config.yaml

@@ -31,7 +31,9 @@ repos:
     rev: v2.2.6
     hooks:
       - id: codespell
-        args: ['--write-changes']
+        args:
+        - --write-changes
+        - --exclude-file=LICENCE
   - repo: https://github.com/PyCQA/doc8
     rev: v1.1.1
     hooks:

CONTRIBUTING.md

+More information on https://atr.pages.teklia.com/contributing/.

Dockerfile

@@ -9,8 +9,7 @@ WORKDIR /src
 
 # Copy DAN data
 COPY dan dan
-COPY requirements.txt *-requirements.txt setup.py VERSION README.md ./
+COPY pyproject.toml README.md ./
 
-# Install DAN as a package with GitLab package registry
-RUN --mount=type=secret,id=netrc,target=/root/.netrc \
-    pip install . --no-cache-dir --index-url https://gitlab.teklia.com/api/v4/projects/210/packages/pypi/simple
+# Install DAN as a package
+RUN pip install . --no-cache-dir

MANIFEST.in

 include LICENSE
-include requirements.txt
-include doc-requirements.txt
-include mlflow-requirements.txt
-include VERSION
+include LICENCE
 include README.md

Makefile

 .PHONY: release
 
 release:
-	$(eval version:=$(shell cat VERSION))
-	echo $(version)
-	git commit VERSION -m "Version $(version)"
+	# Grep the version from pyproject.toml, squeeze multiple spaces, delete double and single quotes, get 3rd val.
+	# This command tolerates multiple whitespace sequences around the version number.
+	$(eval version:=$(shell grep -m 1 version pyproject.toml | tr -s ' ' | tr -d '"' | tr -d "'" | cut -d' ' -f3))
+	echo Releasing version $(version)
+	git commit pyproject.toml -m "Version $(version)"
 	git tag $(version)
 	git push origin main $(version)

README.md

@@ -4,7 +4,7 @@
 
 For more details about this package, make sure to see the documentation available at <https://atr.pages.teklia.com/dan/>.
 
-This is an open-source project, licensed using [the MIT license](https://opensource.org/license/mit/).
+This is an open-source project, licensed using [the CeCILL-C license](https://cecill.info/index.en.html).
 
 ## Inference
 

VERSION

-0.2.0rc4

ci/build.sh

@@ -17,7 +17,7 @@ fi
 IMAGE_TAG="$CI_REGISTRY_IMAGE:$VERSION"
 
 cd $CI_PROJECT_DIR
-docker build -f Dockerfile . -t "$IMAGE_TAG" --secret id=netrc,src=$HOME/.netrc
+docker build -f Dockerfile . -t "$IMAGE_TAG"
 
 # Publish the image on the main branch or on a tag
 if [ "$CI_COMMIT_REF_NAME" = "main" -o -n "$CI_COMMIT_TAG" ]; then

dan/__init__.py

+# Copyright Teklia (contact@teklia.com) & Denis Coquenet
+# This code is licensed under CeCILL-C
+
 # -*- coding: utf-8 -*-
 import logging
 

dan/bio.py

+# Copyright Teklia (contact@teklia.com) & Denis Coquenet
+# This code is licensed under CeCILL-C
+
 """
 Convert DAN predictions to BIO format.
 """

dan/cli.py

+# Copyright Teklia (contact@teklia.com) & Denis Coquenet
+# This code is licensed under CeCILL-C
+
 # -*- coding: utf-8 -*-
 import argparse
 import errno

dan/datasets/__init__.py

+# Copyright Teklia (contact@teklia.com) & Denis Coquenet
+# This code is licensed under CeCILL-C
+
 # -*- coding: utf-8 -*-
 """
 Preprocess datasets for training.

dan/datasets/analyze/__init__.py

+# Copyright Teklia (contact@teklia.com) & Denis Coquenet
+# This code is licensed under CeCILL-C
+
 # -*- coding: utf-8 -*-
 """
 Analyze dataset and display statistics in markdown format.

dan/datasets/analyze/statistics.py

+# Copyright Teklia (contact@teklia.com) & Denis Coquenet
+# This code is licensed under CeCILL-C
+
 # -*- coding: utf-8 -*-
 import logging
 from collections import Counter, defaultdict

dan/datasets/download/__init__.py

+# Copyright Teklia (contact@teklia.com) & Denis Coquenet
+# This code is licensed under CeCILL-C
+
 # -*- coding: utf-8 -*-
 """
 Download images of a dataset from a split extracted by DAN

dan/datasets/download/exceptions.py

+# Copyright Teklia (contact@teklia.com) & Denis Coquenet
+# This code is licensed under CeCILL-C
+
 # -*- coding: utf-8 -*-
 from pathlib import Path