Merge branch 'fix_update_codemeta' into 'master'

Fix update_codemeta, eossr version and skip_ci during CI See merge request !209

Merge branch 'fix_update_codemeta' into 'master'
Fix update_codemeta, eossr version and skip_ci during CI See merge request !209
673dd4db · Vuillaume · 33f94c00 · e4561ebd · 673dd4db · 673dd4db
Commit 673dd4db authored May 04, 2022 by Vuillaume
6 changed files
--- a/.gitlab-ci-update-codemeta.yml
+++ b/.gitlab-ci-update-codemeta.yml
@@ -10,8 +10,6 @@
 #   GITLAB_USERNAME       Username associated with the personal access token.
 #   COMMIT_MESSAGE        Commit message                                        Automatic update of CodeMeta

-stages:
- - update_codemeta


 update_codemeta:
@@ -23,8 +21,12 @@ update_codemeta:
    - git config --global user.email "${GIT_USER_EMAIL:-$GITLAB_USER_EMAIL}"
    - git config --global user.name "${GIT_USER_NAME:-$GITLAB_USER_NAME}"
    - git fetch && git checkout "${CI_MERGE_REQUEST_SOURCE_BRANCH_NAME}"
+    - git config pull.rebase false
+    - git fetch && git checkout "${CI_MERGE_REQUEST_SOURCE_BRANCH_NAME}" && git pull origin "${CI_MERGE_REQUEST_SOURCE_BRANCH_NAME}"

  script:
+    # setuptools_scm needs to be installed before or it can't be used to determine eossr version during install
+    - pip install setuptools_scm
    - pip install .
    - python eossr/scripts/update_codemeta_eossr.py -c codemeta.json
    - cat codemeta.json
@@ -39,7 +41,7 @@ update_codemeta:
        git status

        # Commit all changes
-        git commit -m "Auto-update codemeta.json"
+        git commit -m "Auto-update codemeta.json [skip ci]"

        # Update the repository and make sure to skip the pipeline create for this commit
        git push https://${GITLAB_USERNAME}:${GITLAB_TOKEN}@${CI_SERVER_HOST}/${CI_PROJECT_PATH}.git "${CI_MERGE_REQUEST_SOURCE_BRANCH_NAME}" -o ci.skip

--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
 stages:
 - install
 - test
+ - update_codemeta
+ - test_codemeta
 - build_containers
 - zenodo
 - deploy_pages
 - pypi_publish
- - update_codemeta
-
+ 
 include: '.gitlab-ci-update-codemeta.yml'

 .junit_template: &junit_definition
@@ -19,7 +20,7 @@ install:
  stage: install
  image: python:slim
  script:
-    - apt-get -y update
+    - apt-get -y update && apt-get install git -y
    - pip install --upgrade pip
    - pip install .
    - eossr-codemeta2zenodo --help
@@ -33,7 +34,7 @@ test:
  stage: test
  image: python:slim
  script:
-    - apt-get -y update
+    - apt-get -y update && apt-get install git -y
    - pip install -e ".[tests]"
    - pytest eossr/
      --junitxml=junit_py37.xml
@@ -60,7 +61,7 @@ test_ci_eossr:


 test_codemeta_ingestion:
-  stage: test
+  stage: test_codemeta
  image: gitlab-registry.in2p3.fr/escape2020/wp3/eossr:dev
  script:
    - eossr-check-connection-zenodo --token $ZENODO_TOKEN -p $CI_PROJECT_DIR

--- a/Dockerfile
+++ b/Dockerfile
@@ -2,7 +2,7 @@ FROM docker.io/python:3.8-slim

 SHELL [ "/bin/bash", "-c"]

-RUN apt update
+RUN apt update &&  apt-get install -y git
 COPY . eossr
 RUN pip install "./eossr"
 RUN rm -rf eossr

--- a/codemeta.json
+++ b/codemeta.json
@@ -2,10 +2,10 @@
    "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
    "@type": "SoftwareSourceCode",
    "name": "eossr",
-    "description": "<p align=\"left\"><img src=\"docs/images/eossr_logo.png\" width=\"400px\" ></p><h1>The ESCAPE OSSR library</h1><p>The eOSSR Python library gathers all the developments made for the OSSR. In particular, it includes:- an API to programmatically access the OSSR, retrieve records and publish content- functions to map and crosswalk metadata between the CodeMeta schema adopted for the OSSR and Zenodo internal schema- functions to help developers automatically contribute to the OSSR, in particular using their continuous integration (see also code snippets)</p><p>Code: <a href=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr\">https://gitlab.in2p3.fr/escape2020/wp3/eossr</a>Documentation: <a href=\"https://escape2020.pages.in2p3.fr/wp3/eossr/\">https://escape2020.pages.in2p3.fr/wp3/eossr/</a></p><p><a href=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/commits/master\"><img alt=\"\" src=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/badges/master/pipeline.svg\" /></a><a href=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/commits/master\"><img alt=\"\" src=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/badges/master/coverage.svg\" /></a><a href=\"https://bestpractices.coreinfrastructure.org/projects/5712\"><img alt=\"CII Best Practices\" src=\"https://bestpractices.coreinfrastructure.org/projects/5712/badge\" /></a><a href=\"https://opensource.org/licenses/MIT\"><img alt=\"\" src=\"https://img.shields.io/badge/License-MIT-blue.svg\" /></a><a href=\"https://doi.org/10.5281/zenodo.5524912\"><img alt=\"\" src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.5524912.svg\" /></a><a href=\"https://mybinder.org/v2/git/https%3A%2F%2Fgitlab.in2p3.fr%2Fescape2020%2Fwp3%2Feossr/HEAD\"><img alt=\"\" src=\"https://mybinder.org/badge_logo.svg\" /></a></p><h2>Former stable versions</h2><ul><li>v0.5: <a href=\"https://doi.org/10.5281/zenodo.6352039\"><img alt=\"DOI\" src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.6352039.svg\" /></a></li><li>v0.4: <a href=\"https://doi.org/10.5281/zenodo.6326454\"><img alt=\"DOI\" src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.6326454.svg\" /></a></li><li>v0.3.3: <a href=\"https://doi.org/10.5281/zenodo.5592584\"><img alt=\"\" src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.5592584.svg\" /></a></li><li>v0.2 : <a href=\"https://doi.org/10.5281/zenodo.5524913\"><img alt=\"\" src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.5524913.svg\" /></a></li></ul><h2>Install</h2><p>Commands to be run in your terminal.</p><h3>For users</h3><pre><code>pip install eossr</code></pre><p>You can also run it with docker:</p><pre><code>docker run -it gitlab-registry.in2p3.fr/escape2020/wp3/eossr:latest</code></pre><p><a href=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/container_registry\">Visit our registry</a> to see the available docker containers.</p><p>Note that <code>latest</code> tag always point to the latest stable released container.</p><h3>For developers</h3><pre><code>git clone https://gitlab.in2p3.fr/escape2020/wp3/eossr.gitpip install -e &quot;./eossr&quot;</code></pre><h4>Running tests</h4><p>To run tests locally, run:</p><pre><code>pip install -e &quot;./eossr[tests]&quot;pytest eossr</code></pre><p>Some tests will be skiped if <code>SANDBOX_ZENODO_TOKEN</code> is not defined in your environment variables.If you want to run these tests, you will need to create a <a href=\"https://sandbox.zenodo.org/account/settings/applications/tokens/new/\">sandbox zenodo token</a> and add it to your env:</p><pre><code>export SANDBOX_ZENODO_TOKEN=&quot;your_sandbox_token&quot;</code></pre><h2>License</h2><p>See <a href=\"LICENSE\">LICENSE</a></p><h2>Cite</h2><p>To cite this library, use the cite section in <a href=\"https://zenodo.org/record/5592584#.YiALJRPMI-Q\">the Zenodo page</a> (rightcolumn, below the <code>Versions</code> section).</p>",
+    "description": "<p align=\"left\"><img src=\"docs/images/eossr_logo.png\" width=\"400px\" ></p><h1>The ESCAPE OSSR library</h1><p>The eOSSR Python library gathers all the developments made for the OSSR. In particular, it includes:- an API to programmatically access the OSSR, retrieve records and publish content- functions to map and crosswalk metadata between the CodeMeta schema adopted for the OSSR and Zenodo internal schema- functions to help developers automatically contribute to the OSSR, in particular using their continuous integration (see also code snippets)</p><p>Code: <a href=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr\">https://gitlab.in2p3.fr/escape2020/wp3/eossr</a>Documentation: <a href=\"https://escape2020.pages.in2p3.fr/wp3/eossr/\">https://escape2020.pages.in2p3.fr/wp3/eossr/</a></p><p><a href=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/commits/master\"><img alt=\"\" src=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/badges/master/pipeline.svg\" /></a><a href=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/commits/master\"><img alt=\"\" src=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/badges/master/coverage.svg\" /></a><a href=\"https://bestpractices.coreinfrastructure.org/projects/5712\"><img alt=\"CII Best Practices\" src=\"https://bestpractices.coreinfrastructure.org/projects/5712/badge\" /></a><a href=\"https://opensource.org/licenses/MIT\"><img alt=\"\" src=\"https://img.shields.io/badge/License-MIT-blue.svg\" /></a><a href=\"https://doi.org/10.5281/zenodo.5524912\"><img alt=\"\" src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.5524912.svg\" /></a><a href=\"https://mybinder.org/v2/git/https%3A%2F%2Fgitlab.in2p3.fr%2Fescape2020%2Fwp3%2Feossr/HEAD\"><img alt=\"\" src=\"https://mybinder.org/badge_logo.svg\" /></a></p><h2>Former stable versions</h2><ul><li>v0.6: <a href=\"https://doi.org/10.5281/zenodo.6475946\"><img alt=\"DOI\" src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.6475946.svg\" /></a></li><li>v0.5: <a href=\"https://doi.org/10.5281/zenodo.6352039\"><img alt=\"DOI\" src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.6352039.svg\" /></a></li><li>v0.4: <a href=\"https://doi.org/10.5281/zenodo.6326454\"><img alt=\"DOI\" src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.6326454.svg\" /></a></li><li>v0.3.3: <a href=\"https://doi.org/10.5281/zenodo.5592584\"><img alt=\"\" src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.5592584.svg\" /></a></li><li>v0.2 : <a href=\"https://doi.org/10.5281/zenodo.5524913\"><img alt=\"\" src=\"https://zenodo.org/badge/DOI/10.5281/zenodo.5524913.svg\" /></a></li></ul><h2>Install</h2><p>Commands to be run in your terminal.</p><h3>For users</h3><pre><code>pip install eossr</code></pre><p>You can also run it with docker:</p><pre><code>docker run -it gitlab-registry.in2p3.fr/escape2020/wp3/eossr:latest</code></pre><p><a href=\"https://gitlab.in2p3.fr/escape2020/wp3/eossr/container_registry\">Visit our registry</a> to see the available docker containers.</p><p>Note that <code>latest</code> tag always point to the latest stable released container.</p><h3>For developers</h3><pre><code>git clone https://gitlab.in2p3.fr/escape2020/wp3/eossr.gitpip install -e &quot;./eossr&quot;</code></pre><h4>Running tests</h4><p>To run tests locally, run:</p><pre><code>pip install -e &quot;./eossr[tests]&quot;pytest eossr</code></pre><p>Some tests will be skiped if <code>SANDBOX_ZENODO_TOKEN</code> is not defined in your environment variables.If you want to run these tests, you will need to create a <a href=\"https://sandbox.zenodo.org/account/settings/applications/tokens/new/\">sandbox zenodo token</a> and add it to your env:</p><pre><code>export SANDBOX_ZENODO_TOKEN=&quot;your_sandbox_token&quot;</code></pre><h2>License</h2><p>See <a href=\"LICENSE\">LICENSE</a></p><h2>Cite</h2><p>To cite this library, use the cite section in <a href=\"https://zenodo.org/record/5592584#.YiALJRPMI-Q\">the Zenodo page</a> (rightcolumn, below the <code>Versions</code> section).</p>",
    "license": "https://spdx.org/licenses/MIT",
-    "version": "v0.6",
-    "softwareVersion": "v0.6",
+    "version": "v0.7.dev32+g33d2f4f",
+    "softwareVersion": "v0.7.dev32+g33d2f4f",
    "codeRepository": "https://gitlab.in2p3.fr/escape2020/wp3/eossr",
    "developmentStatus": "active",
    "isAccessibleForFree": true,
@@ -43,11 +43,11 @@
        "zenodo"
    ],
    "runtimePlatform": "Python 3",
-    "downloadUrl": "https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/archive/v0.6/eossr-v0.6.zip",
+    "downloadUrl": "https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/archive/v0.7.dev32+g33d2f4f/eossr-v0.7.dev32+g33d2f4f.zip",
    "releaseNotes": "eossr v0.6 Minor bug fixes and documentation improvements. Full changelog: https://gitlab.in2p3.fr/escape2020/wp3/eossr/-/releases/v0.6",
    "dateCreated": "2021-08-31",
-    "datePublished": "2022-04-22",
-    "dateModified": "2022-04-22",
+    "datePublished": "2022-05-04",
+    "dateModified": "2022-05-04",
    "operatingSystem": "",
    "maintainer": {
        "@type": "Person",

--- a/eossr/tests/test_utils.py
+++ b/eossr/tests/test_utils.py
@@ -65,8 +65,12 @@ def test_zip_repository():
            )


-def test_readme_to_html():
-    eutils.markdown_to_html()
+def test_markdown_to_html():
+    with tempfile.TemporaryDirectory() as tmpdir:
+        _, tmpfile = tempfile.mkstemp()
+        Path(tmpfile).write_text("# Hello Markdown")
+        html = eutils.markdown_to_html(tmpfile)
+    assert html == '<h1>Hello Markdown</h1>'


 def test_update_codemeta():

--- a/eossr/version.py
+++ b/eossr/version.py
 # this is adapted from https://github.com/astropy/astropy/blob/master/astropy/version.py
 # see https://github.com/astropy/astropy/pull/10774 for a discussion on why this needed.
+import warnings

 try:
    try:
        from ._dev_version import version
-    except ImportError:
+    except ImportError as e:
+        warnings.warn(e.msg)
        from ._version import __version__ as version
 except Exception as e:
-    import warnings
-
    warnings.warn(
        "Could not determine eossr version; this indicates a broken installation."
        " Install eossr from PyPI, a local git repository or using "
        " pip install git+https://gitlab.in2p3.fr/escape2020/wp3/eossr@VERSION "
-        " Installing github's autogenerated source release tarballs "
+        " Installing gitlab's autogenerated source release tarballs "
        " does not include version information and should be avoided."
        f"Exception Error: {e}"
    )
-    del warnings
    version = "0.0.0"

 __version__ = version