Merge branch 'release-0.6.1' into 'main'

DOC: Added CITATION.cff to the list of files in the release guide where the...

See merge request !65

.gitlab-ci.yml

@@ -25,7 +25,7 @@ variables:
    CI_REGISTRY_IMAGE_BASE: $CI_REGISTRY/caosdb/src/caosdb-advanced-user-tools/base:latest
 
 
-stages: 
+stages:
   - setup
   - cert
   - style
@@ -53,15 +53,15 @@ test:
       - time docker load < /image-cache/mariadb.tar || true
       - time docker load < /image-cache/caosdb-dev.tar || true
       - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN $CI_REGISTRY
-      - EXEPATH=`pwd` CAOSDB_TAG=$CAOSDB_TAG docker-compose 
+      - EXEPATH=`pwd` CAOSDB_TAG=$CAOSDB_TAG docker-compose
         -f .docker/docker-compose.yml up -d
-      - cd .docker 
+      - cd .docker
       - /bin/sh ./run.sh
-      - cd .. 
+      - cd ..
       - docker logs docker-caosdb-server-1 &> caosdb_log.txt
       - docker logs docker-sqldb-1 &> mariadb_log.txt
       - docker-compose -f .docker/docker-compose.yml down
-      - rc=`cat .docker/result`  
+      - rc=`cat .docker/result`
       - exit $rc
   dependencies: [cert]
   needs: [cert]
@@ -76,19 +76,19 @@ build-testenv:
   tags: [cached-dind]
   image: docker:18.09
   stage: setup
-  # Hint: do not use only here; the image needs always to be build since it 
+  # Hint: do not use only here; the image needs always to be build since it
   # contains the repo code
   #only:
-  script: 
+  script:
       - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN $CI_REGISTRY
         # use here general latest or specific branch latest...
-      - docker build 
+      - docker build
         --file .docker/Dockerfile
         -t $CI_REGISTRY_IMAGE .
       - docker push $CI_REGISTRY_IMAGE
       - docker save $CI_REGISTRY_IMAGE > /image-cache/caosdb-advanced-testenv.tar
       - cd .docker-base
-      - docker build 
+      - docker build
         -t $CI_REGISTRY_IMAGE_BASE .
       - docker push $CI_REGISTRY_IMAGE_BASE
 
@@ -123,14 +123,45 @@ linting:
       - make lint
   allow_failure: true
 
-unittest:
+unittest_py39:
   tags: [docker]
   stage: unittest
   image: $CI_REGISTRY_IMAGE
   needs: [build-testenv]
   script:
-      - python3 -c "import caosdb; print('CaosDB Version:', caosdb.__version__)"
-      - tox
+    # First verify that system Python actually is 3.9
+    - python3 -c "import sys; assert sys.version.startswith('3.9')"
+    - python3 -c "import caosdb; print('CaosDB Version:', caosdb.__version__)"
+    - tox
+
+unittest_py37:
+  tags: [docker]
+  stage: unittest
+  image: python:3.7
+  script: &python_test_script
+    - pip install nose pandas pytest pytest-cov gitignore-parser openpyxl>=3.0.7 xlrd==1.2 h5py
+    - pip install git+https://gitlab.indiscale.com/caosdb/src/caosdb-pylib.git@dev
+    - pip install .
+    - pytest --cov=caosadvancedtools unittests
+
+unittest_py38:
+  tags: [docker]
+  stage: unittest
+  image: python:3.8
+  script: *python_test_script
+
+unittest_py310:
+  tags: [docker]
+  stage: unittest
+  image: python:3.10
+  script: *python_test_script
+
+unittest_py311:
+  tags: [docker]
+  stage: unittest
+  image: python:3.11
+  script: *python_test_script
+  allow_failure: true
 
 # Build the sphinx documentation and make it ready for deployment by Gitlab Pages
 # Special job for serving a static website. See https://docs.gitlab.com/ee/ci/yaml/README.html#pages

CHANGELOG.md

@@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.6.1] - 2023-01-20##
+
+### Added ###
+
+* Re-introduced support for Python 3.7
+
 ## [0.6.0] - 2022-10-11 ##
 (Florian Spreckelsen)
 

CITATION.cff

+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: Fitschen
+    given-names: Timm
+    orcid: https://orcid.org/0000-0002-4022-432X
+  - family-names: Schlemmer
+    given-names: Alexander
+    orcid: https://orcid.org/0000-0003-4124-9649
+  - family-names: Hornung
+    given-names: Daniel
+    orcid: https://orcid.org/0000-0002-7846-6375
+  - family-names: tom Wörden
+    given-names: Henrik
+    orcid: https://orcid.org/0000-0002-5549-578X
+  - family-names: Parlitz
+    given-names: Ulrich
+    orcid: https://orcid.org/0000-0003-3058-1435
+  - family-names: Luther
+    given-names: Stefan
+    orcid: https://orcid.org/0000-0001-7214-8125
+title: CaosDB - Advanced User Tools
+version: 0.6.1
+doi: 10.3390/data4020083
+date-released: 2023-01-20
\ No newline at end of file

README.md

@@ -43,7 +43,7 @@ Conduct](https://gitlab.com/caosdb/caosdb/-/blob/dev/CODE_OF_CONDUCT.md).
   [documentation](https://docs.indiscale.com/caosdb-advanced-user-tools/), the
   preferred way is also a merge request as describe above (the documentation
   resides in `src/doc`). However, you can also create an issue for it.
-- You can also contact us at **info (AT) caosdb.de** and join the CaosDB
+- You can also contact us at **info (AT) caosdb.org** and join the CaosDB
   community on
   [#caosdb:matrix.org](https://matrix.to/#/!unwwlTfOznjEnMMXxf:matrix.org).
 

README_SETUP.md

@@ -52,6 +52,8 @@ Optional h5-crawler:
 `make style`
 
 ## Documentation #
+We use sphinx to create the documentation. Docstrings in the code should comply
+with the Googly style (see link below).
 
 Build documentation in `build/` with `make doc`.
 
@@ -60,3 +62,9 @@ Build documentation in `build/` with `make doc`.
 - `sphinx`
 - `sphinx-autoapi`
 - `recommonmark >= 0.6.0`
+
+### How to contribute ###
+
+- [Google Style Python Docstrings](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html)
+- [Google Style Python Docstrings 2nd reference](https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings)
+- [References to other documentation](https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#role-external)

RELEASE_GUIDELINES.md

@@ -24,6 +24,7 @@ guidelines of the CaosDB Project
    - `version` variables in `src/doc/conf.py`
    - Version on [setup.py](./setup.py): Check the `MAJOR`, `MINOR`, `MICRO`, `PRE` variables and set
      `ISRELEASED` to `True`. Use the possibility to issue pre-release versions for testing.
+   - `CITATION.cff` (update version and date)
 
 5. Merge the release branch into the main branch.
 

pytest.ini

-[pytest]
-testpaths = unittests
-addopts = -vv

setup.py

@@ -47,7 +47,7 @@ from setuptools import find_packages, setup
 
 MAJOR = 0
 MINOR = 6
-MICRO = 0
+MICRO = 1
 PRE = ""  # e.g. rc0, alpha.1, 0.beta-23
 ISRELEASED = True
 
@@ -154,7 +154,8 @@ def setup_package():
         long_description_content_type="text/markdown",
         author='Henrik tom Wörden',
         author_email='h.tomwoerden@indiscale.com',
-        install_requires=["caosdb>=0.7.0",
+        python_requires='>=3.7',
+        install_requires=["caosdb>=0.11.0",
                           "jsonschema>=4.4.0",
                           "numpy>=1.17.3",
                           "openpyxl>=3.0.7",

src/caosadvancedtools/models/data_model.py

@@ -141,7 +141,7 @@ class DataModel(dict):
                     # in via the extern keyword:
                     ref = db.Property(name=ent.name).retrieve()
                 else:
-                    query = db.Query(f"FIND * with id={ent.id}")
+                    query = db.Query(f"FIND ENTITY with id={ent.id}")
                     ref = query.execute(unique=True)
                 diff = (describe_diff(*compare_entities(ent, ref
                                                         ), name=ent.name))

src/doc/conf.py

@@ -27,9 +27,9 @@ copyright = '2021, IndiScale GmbH'
 author = 'Daniel Hornung'
 
 # The short X.Y version
-version = '0.6.0'
+version = '0.6.1'
 # The full version, including alpha/beta/rc tags
-release = '0.6.0'
+release = '0.6.1'
 
 
 # -- General configuration ---------------------------------------------------

tox.ini

 [tox]
-envlist=py36, py37, py38, py39, py310
+envlist=py37, py38, py39, py310, py311
 skip_missing_interpreters = true
+
 [testenv]
 deps=nose
     pandas
@@ -15,3 +16,8 @@ commands=py.test --cov=caosadvancedtools -vv {posargs}
 
 [flake8]
 max-line-length=100
+
+[pytest]
+testpaths = unittests
+addopts = -vv
+xfail_strict = True