Fix/update dependencies gdev 1568 (#39)

* Updated dependencies + template
ghga-de · Jan 24, 2023 · 4acdaca · 4acdaca
1 parent 605c266
commit 4acdaca
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diff --git a/.aws/config b/.aws/config
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/.aws/credentials b/.aws/credentials
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/.deprecated_files b/.deprecated_files
@@ -0,0 +1,13 @@
+# List of all deprecated files and directories that
+# should not exist any more in this repo.
+# This list is similar to the `./mandatory_files`,
+# however, the entries here will be removed if they
+# still exist.
+
+.devcontainer/library-scripts/docker-in-docker-debian.sh
+.devcontainer/library-scripts
+
+.github/workflows/check_mandatory_and_static_files.yaml
+
+scripts/check_mandatory_and_static_files.py
+scripts/update_static_files.py
diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
@@ -20,11 +20,4 @@ RUN if [ "${INSTALL_NODE}" = "true" ]; then su vscode -c "umask 0002 && . /usr/l
 # Copy install and launcher script to bin:
 COPY ./dev_install /bin
 
-# make docker in docker work:
-# (https://github.com/microsoft/vscode-dev-containers/blob/main/script-library/docs/docker-in-docker.md#script-use)
-COPY library-scripts/*.sh /tmp/library-scripts/
-ENV DOCKER_BUILDKIT=1
-RUN apt-get update && /bin/bash /tmp/library-scripts/docker-in-docker-debian.sh
-ENTRYPOINT ["/usr/local/share/docker-init.sh"]
-VOLUME [ "/var/lib/docker" ]
 CMD ["sleep", "infinity"]
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -71,9 +71,11 @@
 	// Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
 	"remoteUser": "vscode",
 	"features": {
-		"docker-in-docker": {
+		"ghcr.io/devcontainers/features/docker-in-docker:2": {
 			"version": "latest",
-			"moby": true
+			"enableNonRootDocker": "true",
+			"moby": true,
+			"azureDnsAutoDetection": false
 		}
 	}
 }
diff --git a/.devcontainer/library-scripts/docker-in-docker-debian.sh b/.devcontainer/library-scripts/docker-in-docker-debian.sh
diff --git a/.devcontainer/license_header.txt b/.devcontainer/license_header.txt
@@ -1,4 +1,4 @@
-Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 for the German Human Genome-Phenome Archive (GHGA)
 
 Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/.flake8 b/.flake8
@@ -1,4 +1,4 @@
-; Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+; Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 ; for the German Human Genome-Phenome Archive (GHGA)
 ;
 ; Licensed under the Apache License, Version 2.0 (the "License");
@@ -14,7 +14,8 @@
 ; limitations under the License.
 
 [flake8]
-ignore = E, W # ignore all style checks from pycodestyle
-              # as they are already checked by black
+ignore = E, W
+    # ignore all style checks from pycodestyle
+    # as they are already checked by black
 exclude = .git,__pycache__,build,dist
 max-complexity = 10
diff --git a/.github/workflows/check_config_docs.yaml b/.github/workflows/check_config_docs.yaml
@@ -6,10 +6,10 @@ jobs:
   static-code-analysis:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2.4.2
+      - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/[email protected].2
+        uses: ghga-de/[email protected].3
 
       - name: Check config docs
         run: |

diff --git a/...ows/check_mandatory_and_static_files.yaml → .github/workflows/check_template_files.yaml b/...ows/check_mandatory_and_static_files.yaml → .github/workflows/check_template_files.yaml
@@ -1,21 +1,21 @@
-name: Check mandatory and static files
+name: Check template files
 
 on: push
 
 jobs:
-  check-mandatory-and-static-files:
+  check-template-files:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2.4.2
+      - uses: actions/checkout@v3
       - name: Set up Python 3.9
-        uses: actions/setup-python@v3.1.2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
-      - name: Check mandatory and static files
+      - name: Check template files
         run: |
           if [ "${{ github.event.repository.name }}" == "microservice-repository-template" ]
           then
             echo "Skipping this test as operating on the template repo."
           else
-            ./scripts/check_mandatory_and_static_files.py
+            ./scripts/update_template_files.py --check
           fi
diff --git a/.github/workflows/static_code_analysis.yaml b/.github/workflows/static_code_analysis.yaml
@@ -7,13 +7,13 @@ jobs:
     runs-on: ubuntu-latest
     name: Static Code Analysis
     steps:
-      - uses: actions/checkout@v2.4.2
+      - uses: actions/checkout@v3
       - name: Retrieve main src dir
         id: main_src_dir
         run: |
-          echo "::set-output name=MAIN_SRC_DIR::${PWD}/$(./scripts/get_package_name.py)"
+          echo "MAIN_SRC_DIR=${PWD}/$(./scripts/get_package_name.py)" >> $GITHUB_OUTPUT
       - name: Set up Python 3.9
-        uses: actions/setup-python@v3.1.2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.9
       - name: Install Dependencies

diff --git a/.github/workflows/unit_and_int_tests.yaml b/.github/workflows/unit_and_int_tests.yaml
@@ -8,10 +8,10 @@ jobs:
     name: Unit and Integration Tests
 
     steps:
-      - uses: actions/checkout@v2.4.2
+      - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/[email protected].2
+        uses: ghga-de/[email protected].3
 
       - name: Run pytest
         run: |

diff --git a/.mandatory_files b/.mandatory_files
@@ -6,20 +6,23 @@
 # may differ from that of the template repository.
 
 .devcontainer/dev_install
+.devcontainer/dev_launcher
 .devcontainer/devcontainer.json
 .devcontainer/docker-compose.yml
 .devcontainer/Dockerfile
 
-.github/workflows/unit_and_int_tests.yaml
-.github/workflows/static_code_analysis.yaml
+.github/workflows/dev_cd.yaml
 .github/workflows/unit_and_int_tests.yaml
 
 docs/README.md
 
 example_data
 
+tests/__init__.py
+tests/fixtures/__init__.py
+
+Dockerfile
+config_schema.json
+example_config.yaml
 README.md
 setup.py
-
-.mandatory_files
-.static_files
diff --git a/.mandatory_files_ignore b/.mandatory_files_ignore
@@ -0,0 +1,10 @@
+# Optional list of files which are actually mandatory in the template
+# but are allowed to be removed in the current repository
+.devcontainer/dev_launcher
+.github/workflows/dev_cd.yaml
+.github/workflows/unit_and_int_tests.yaml
+Dockerfile
+config_schema.json
+example_config.yaml
+tests/__init__.py
+tests/fixtures/__init__.py
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,11 +4,11 @@
 default_language_version:
   python: python3.9
 
-minimum_pre_commit_version: 2.13.0
+minimum_pre_commit_version: 2.17.0
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.4.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -37,27 +37,27 @@ repos:
       - id: debug-statements
       - id: debug-statements
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 22.12.0
     hooks:
       - id: black
   - repo: https://github.com/pycqa/isort
-    rev: 5.10.1
+    rev: 5.11.4
     hooks:
       - id: isort
         args: [--profile, black]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.981
+    rev: v0.991
     hooks:
       - id: mypy
         args: [--no-warn-unused-ignores]
   - repo: https://github.com/PyCQA/pylint
-    rev: v2.13.3
+    rev: v2.15.10
     hooks:
       - id: pylint
         args: [--disable=E0401]
         exclude: tests|.devcontainer
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 6.0.0
     hooks:
       - id: flake8
         args: [--config, .flake8]

diff --git a/.pylintrc b/.pylintrc
@@ -238,6 +238,7 @@ good-names=i,
            j,
            k,
            ex,
+           ok,
            Run,
            _,
            __,

diff --git a/.static_files b/.static_files
@@ -8,16 +8,21 @@
 # your repo by running the script at:
 # ./scripts/update_static_files.py
 
-.devcontainer/library-scripts/docker-in-docker-debian.sh
 .devcontainer/license_header.txt
 
-scripts/update_static_files.py
+scripts/script_utils/__init__.py
+scripts/script_utils/cli.py
+
 scripts/license_checker.py
 scripts/get_package_name.py
-scripts/check_mandatory_and_static_files.py
+scripts/update_config_docs.py
+scripts/update_template_files.py
 scripts/README.md
 
-.github/workflows/check_mandatory_and_static_files.yaml
+.github/workflows/check_config_docs.yaml
+.github/workflows/check_template_files.yaml
+.github/workflows/static_code_analysis.yaml
+.github/workflows/unit_and_int_tests.yaml
 
 example_data/README.md
 
@@ -28,6 +33,7 @@ example_data/README.md
 .pre-commit-config.yaml
 .pylintrc
 .mypy.ini
+pytest.ini
 
 LICENSE
 requirements.txt

diff --git a/.static_files_ignore b/.static_files_ignore
@@ -0,0 +1,9 @@
+# Optional list of files which are actually static in the template
+# but are allowed to have different content in the current repository
+.github/workflows/check_config_docs.yaml
+.github/workflows/static_code_analysis.yaml
+.github/workflows/unit_and_int_tests.yaml
+pytest.ini
+scripts/script_utils/__init__.py
+scripts/script_utils/cli.py
+scripts/update_config_docs.py
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/LICENSE b/LICENSE
@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+   Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
    for the German Human Genome-Phenome Archive (GHGA)
 
    Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/ghga_connector/__init__.py b/ghga_connector/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,4 +17,4 @@
 CLI - Client to perform up- and download operations to and from a local ghga instance
 """
 
-__version__ = "0.2.4"
+__version__ = "0.2.5"
diff --git a/ghga_connector/__main__.py b/ghga_connector/__main__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/ghga_connector/cli.py b/ghga_connector/cli.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/ghga_connector/config.py b/ghga_connector/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/ghga_connector/core/__init__.py b/ghga_connector/core/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/ghga_connector/core/api_calls.py b/ghga_connector/core/api_calls.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/ghga_connector/core/constants.py b/ghga_connector/core/constants.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/ghga_connector/core/exceptions.py b/ghga_connector/core/exceptions.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/ghga_connector/core/file_operations.py b/ghga_connector/core/file_operations.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/ghga_connector/core/http_translation.py b/ghga_connector/core/http_translation.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/ghga_connector/core/main.py b/ghga_connector/core/main.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/ghga_connector/core/message_display.py b/ghga_connector/core/message_display.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");

diff --git a/ghga_connector/core/session.py b/ghga_connector/core/session.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2022 Universität Tübingen, DKFZ and EMBL
+# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
-Original file line number
+Diff line change
@@ Expand Up / @@ -238,6 +238,7 @@ good-names=i, @@
                j,
                k,
                ex,
+               ok,
                Run,
                _,
                __,
@@ Expand Down @@