From 2f620009ddc0fd8a1047a5fb49ff40e08bb3306a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Jan 2023 08:14:35 +0000 Subject: [PATCH 01/52] Bump coverage from 7.0.4 to 7.0.5 Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.0.4 to 7.0.5. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](https://github.com/nedbat/coveragepy/compare/7.0.4...7.0.5) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 297700ee..c38f8898 100644 --- a/setup.py +++ b/setup.py @@ -55,7 +55,7 @@ "Cython==0.29.33", ], "test": [ - "coverage==7.0.4", + "coverage==7.0.5", "pytest<7.3", "pytest-cov==4.0.0", "testfixtures==7.0.4", From 07c282d3f79e4402713b6fa503b4321e24ab332b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Jan 2023 08:15:00 +0000 Subject: [PATCH 02/52] Bump tox from 4.2.6 to 4.3.1 Bumps [tox](https://github.com/tox-dev/tox) from 4.2.6 to 4.3.1. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.2.6...4.3.1) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 297700ee..8fe309a9 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.3", "pytest-cov==4.0.0", "testfixtures==7.0.4", - "tox==4.2.6", + "tox==4.3.1", "flake8==6.0.0", "flake8-docstrings==1.6.0", "aioresponses==0.7.4", From 2b2c9ed31675eec528a7fdab2c120734fef8871d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Jan 2023 23:01:16 +0000 Subject: [PATCH 03/52] Bump tox from 4.3.1 to 4.3.3 Bumps [tox](https://github.com/tox-dev/tox) from 4.3.1 to 4.3.3. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.3.1...4.3.3) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 6d6795ef..18890f07 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.3", "pytest-cov==4.0.0", "testfixtures==7.0.4", - "tox==4.3.1", + "tox==4.3.3", "flake8==6.0.0", "flake8-docstrings==1.6.0", "aioresponses==0.7.4", From ead733ef87a3c4f2ac5d12b1a66788ade9cf6305 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 23 Jan 2023 12:06:30 +0000 Subject: [PATCH 04/52] Bump tox from 4.3.3 to 4.3.5 Bumps [tox](https://github.com/tox-dev/tox) from 4.3.3 to 4.3.5. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.3.3...4.3.5) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 18890f07..420a625c 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.3", "pytest-cov==4.0.0", "testfixtures==7.0.4", - "tox==4.3.3", + "tox==4.3.5", "flake8==6.0.0", "flake8-docstrings==1.6.0", "aioresponses==0.7.4", From 81e5b5aaaf2000696e48d46d6a670d03ba7ba3db Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 30 Jan 2023 06:52:56 +0000 Subject: [PATCH 05/52] Bump dependabot/fetch-metadata from 1.3.5 to 1.3.6 Bumps [dependabot/fetch-metadata](https://github.com/dependabot/fetch-metadata) from 1.3.5 to 1.3.6. - [Release notes](https://github.com/dependabot/fetch-metadata/releases) - [Commits](https://github.com/dependabot/fetch-metadata/compare/v1.3.5...v1.3.6) --- updated-dependencies: - dependency-name: dependabot/fetch-metadata dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- .github/workflows/dependabot-auto-merge.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dependabot-auto-merge.yml b/.github/workflows/dependabot-auto-merge.yml index ae539537..afa59cc6 100644 --- a/.github/workflows/dependabot-auto-merge.yml +++ b/.github/workflows/dependabot-auto-merge.yml @@ -12,7 +12,7 @@ jobs: steps: - name: Dependabot metadata id: metadata - uses: dependabot/fetch-metadata@v1.3.5 + uses: dependabot/fetch-metadata@v1.3.6 with: github-token: "${{ secrets.GITHUB_TOKEN }}" - name: Wait other jobs are passed or failed From 9111debca1a3d5f17dc21dee12d816bee3980943 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 30 Jan 2023 06:53:04 +0000 Subject: [PATCH 06/52] Bump tox from 4.3.5 to 4.4.2 Bumps [tox](https://github.com/tox-dev/tox) from 4.3.5 to 4.4.2. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.3.5...4.4.2) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 420a625c..b91b8107 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.3", "pytest-cov==4.0.0", "testfixtures==7.0.4", - "tox==4.3.5", + "tox==4.4.2", "flake8==6.0.0", "flake8-docstrings==1.6.0", "aioresponses==0.7.4", From be03cf4c56a9571e1aae31dc39c09bfcf327219c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 30 Jan 2023 06:53:09 +0000 Subject: [PATCH 07/52] Bump flake8-docstrings from 1.6.0 to 1.7.0 Bumps [flake8-docstrings](https://github.com/pycqa/flake8-docstrings) from 1.6.0 to 1.7.0. - [Release notes](https://github.com/pycqa/flake8-docstrings/releases) - [Changelog](https://github.com/PyCQA/flake8-docstrings/blob/main/HISTORY.rst) - [Commits](https://github.com/pycqa/flake8-docstrings/compare/1.6.0...1.7.0) --- updated-dependencies: - dependency-name: flake8-docstrings dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 420a625c..84beb792 100644 --- a/setup.py +++ b/setup.py @@ -61,7 +61,7 @@ "testfixtures==7.0.4", "tox==4.3.5", "flake8==6.0.0", - "flake8-docstrings==1.6.0", + "flake8-docstrings==1.7.0", "aioresponses==0.7.4", "black==22.12.0", ], From 05d692d1f5cf22443addb71c21b6f730199f2e1d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 30 Jan 2023 06:53:17 +0000 Subject: [PATCH 08/52] Bump coverage from 7.0.5 to 7.1.0 Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.0.5 to 7.1.0. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](https://github.com/nedbat/coveragepy/compare/7.0.5...7.1.0) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 420a625c..5b642e11 100644 --- a/setup.py +++ b/setup.py @@ -55,7 +55,7 @@ "Cython==0.29.33", ], "test": [ - "coverage==7.0.5", + "coverage==7.1.0", "pytest<7.3", "pytest-cov==4.0.0", "testfixtures==7.0.4", From b2ef0e0270bcd05c3fb094427ec71b85f26cf16b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 30 Jan 2023 23:01:05 +0000 Subject: [PATCH 09/52] Bump docker/build-push-action from 3 to 4 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 3 to 4. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/v3...v4) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/int.yml | 2 +- .github/workflows/publish.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/int.yml b/.github/workflows/int.yml index d8da464c..92962db3 100644 --- a/.github/workflows/int.yml +++ b/.github/workflows/int.yml @@ -39,7 +39,7 @@ jobs: driver-opts: network=host - name: Build - uses: docker/build-push-action@v3 + uses: docker/build-push-action@v4 with: context: . push: true diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 64a62ef2..7dd68814 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -37,7 +37,7 @@ jobs: type=ref,event=tag - name: Build and push - uses: docker/build-push-action@v3 + uses: docker/build-push-action@v4 with: context: . file: ./Dockerfile @@ -51,7 +51,7 @@ jobs: org.opencontainers.image.revision=${{ github.sha }} - name: Build and push dataloader - uses: docker/build-push-action@v3 + uses: docker/build-push-action@v4 with: run: | pushd deploy/dataloader From 940b6d1d63bcfcf2ca16b371074e1ed72b918894 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 6 Feb 2023 08:21:46 +0000 Subject: [PATCH 10/52] Bump black from 22.12.0 to 23.1.0 Bumps [black](https://github.com/psf/black) from 22.12.0 to 23.1.0. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](https://github.com/psf/black/compare/22.12.0...23.1.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index e34c8c77..15427beb 100644 --- a/setup.py +++ b/setup.py @@ -63,7 +63,7 @@ "flake8==6.0.0", "flake8-docstrings==1.7.0", "aioresponses==0.7.4", - "black==22.12.0", + "black==23.1.0", ], "docs": ["sphinx >= 1.4", "sphinx_rtd_theme==1.1.1"], }, From 6cbc3bde9f3d311e6c173ff5979b15f8e8c211b3 Mon Sep 17 00:00:00 2001 From: Stefan Negru Date: Mon, 6 Feb 2023 10:24:59 +0200 Subject: [PATCH 11/52] fix black formatting --- beacon_api/extensions/mate_name.py | 1 - 1 file changed, 1 deletion(-) diff --git a/beacon_api/extensions/mate_name.py b/beacon_api/extensions/mate_name.py index 149a4d81..83fceb62 100644 --- a/beacon_api/extensions/mate_name.py +++ b/beacon_api/extensions/mate_name.py @@ -45,7 +45,6 @@ async def fetch_fusion_dataset(db_pool, assembly_id, position, chromosome, refer db_response = await statement.fetch(datasets_query, access_query, assembly_id, chromosome) else: - # UBER QUERY - TBD if it is what we need # referenceBases, alternateBases and variantType fields are NOT part of beacon's specification response query = """SELECT a.datasetId as "datasetId", b.accessType as "accessType", a.chromosome as "referenceName", From 256316f2c1a7ef72f12ec21e7dbe28d8b2aedfaf Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 6 Feb 2023 09:08:50 +0000 Subject: [PATCH 12/52] Bump tox from 4.4.2 to 4.4.4 Bumps [tox](https://github.com/tox-dev/tox) from 4.4.2 to 4.4.4. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.4.2...4.4.4) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 15427beb..a1d8ddef 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.3", "pytest-cov==4.0.0", "testfixtures==7.0.4", - "tox==4.4.2", + "tox==4.4.4", "flake8==6.0.0", "flake8-docstrings==1.7.0", "aioresponses==0.7.4", From 581db57dbbae63b0ce51758e7c42997ddd02a1a3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 6 Feb 2023 09:09:09 +0000 Subject: [PATCH 13/52] Bump numpy from 1.24.1 to 1.24.2 Bumps [numpy](https://github.com/numpy/numpy) from 1.24.1 to 1.24.2. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v1.24.1...v1.24.2) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 15427beb..de92ebb1 100644 --- a/setup.py +++ b/setup.py @@ -50,7 +50,7 @@ ], extras_require={ "vcf": [ - "numpy==1.24.1", + "numpy==1.24.2", "cyvcf2==0.30.18", "Cython==0.29.33", ], From 13ab442961746625340689ebaeaa36b73641b98f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 13 Feb 2023 09:28:34 +0000 Subject: [PATCH 14/52] Bump tox from 4.4.4 to 4.4.5 Bumps [tox](https://github.com/tox-dev/tox) from 4.4.4 to 4.4.5. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.4.4...4.4.5) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 4855c63a..952a0242 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.3", "pytest-cov==4.0.0", "testfixtures==7.0.4", - "tox==4.4.4", + "tox==4.4.5", "flake8==6.0.0", "flake8-docstrings==1.7.0", "aioresponses==0.7.4", From d7463199645bfb7d505de315eb8098c8dff2299d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 13 Feb 2023 09:28:41 +0000 Subject: [PATCH 15/52] Bump aiohttp from 3.8.3 to 3.8.4 Bumps [aiohttp](https://github.com/aio-libs/aiohttp) from 3.8.3 to 3.8.4. - [Release notes](https://github.com/aio-libs/aiohttp/releases) - [Changelog](https://github.com/aio-libs/aiohttp/blob/master/CHANGES.rst) - [Commits](https://github.com/aio-libs/aiohttp/compare/v3.8.3...v3.8.4) --- updated-dependencies: - dependency-name: aiohttp dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 4b8e87eb..00c29935 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -aiohttp==3.8.3 +aiohttp==3.8.4 aiohttp-cors==0.7.0 asyncpg==0.27.0 jsonschema==4.17.3 diff --git a/setup.py b/setup.py index 4855c63a..f5e8e1a2 100644 --- a/setup.py +++ b/setup.py @@ -38,7 +38,7 @@ ], install_requires=[ "asyncpg==0.27.0", - "aiohttp==3.8.3", + "aiohttp==3.8.4", "Authlib==1.2.0", "aiohttp-cors==0.7.0", "jsonschema==4.17.3", From 02e1966cea59e551116641f9ca971f25dc4fa0bb Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 13 Feb 2023 09:28:47 +0000 Subject: [PATCH 16/52] Bump sphinx-rtd-theme from 1.1.1 to 1.2.0 Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.1.1 to 1.2.0. - [Release notes](https://github.com/readthedocs/sphinx_rtd_theme/releases) - [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst) - [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/1.1.1...1.2.0) --- updated-dependencies: - dependency-name: sphinx-rtd-theme dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 4855c63a..6141bf22 100644 --- a/setup.py +++ b/setup.py @@ -65,6 +65,6 @@ "aioresponses==0.7.4", "black==23.1.0", ], - "docs": ["sphinx >= 1.4", "sphinx_rtd_theme==1.1.1"], + "docs": ["sphinx >= 1.4", "sphinx_rtd_theme==1.2.0"], }, ) From aa8084766d26a660d0f4120edb00a77d531649ad Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 13 Feb 2023 09:45:38 +0000 Subject: [PATCH 17/52] Bump testfixtures from 7.0.4 to 7.1.0 Bumps [testfixtures](https://github.com/Simplistix/testfixtures) from 7.0.4 to 7.1.0. - [Release notes](https://github.com/Simplistix/testfixtures/releases) - [Changelog](https://github.com/simplistix/testfixtures/blob/master/CHANGELOG.rst) - [Commits](https://github.com/Simplistix/testfixtures/compare/7.0.4...7.1.0) --- updated-dependencies: - dependency-name: testfixtures dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 952a0242..465446af 100644 --- a/setup.py +++ b/setup.py @@ -58,7 +58,7 @@ "coverage==7.1.0", "pytest<7.3", "pytest-cov==4.0.0", - "testfixtures==7.0.4", + "testfixtures==7.1.0", "tox==4.4.5", "flake8==6.0.0", "flake8-docstrings==1.7.0", From 61eb0f00dad8b67a2e9b78bf62cb454316ffe08e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 20 Feb 2023 23:56:42 +0000 Subject: [PATCH 18/52] Bump rojopolis/spellcheck-github-actions from 0.29.0 to 0.30.0 Bumps [rojopolis/spellcheck-github-actions](https://github.com/rojopolis/spellcheck-github-actions) from 0.29.0 to 0.30.0. - [Release notes](https://github.com/rojopolis/spellcheck-github-actions/releases) - [Changelog](https://github.com/rojopolis/spellcheck-github-actions/blob/master/CHANGELOG.md) - [Commits](https://github.com/rojopolis/spellcheck-github-actions/compare/0.29.0...0.30.0) --- updated-dependencies: - dependency-name: rojopolis/spellcheck-github-actions dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 6925a9c3..2e6fc6e6 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -13,7 +13,7 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: rojopolis/spellcheck-github-actions@0.29.0 + - uses: rojopolis/spellcheck-github-actions@0.30.0 name: Spellcheck code_docs: From b19d55407ddd901dcfde23f4f601a4d21a77bbc3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 27 Feb 2023 23:56:59 +0000 Subject: [PATCH 19/52] Bump coverage from 7.1.0 to 7.2.1 Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.1.0 to 7.2.1. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](https://github.com/nedbat/coveragepy/compare/7.1.0...7.2.1) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 47b3af5e..5d653548 100644 --- a/setup.py +++ b/setup.py @@ -55,7 +55,7 @@ "Cython==0.29.33", ], "test": [ - "coverage==7.1.0", + "coverage==7.2.1", "pytest<7.3", "pytest-cov==4.0.0", "testfixtures==7.1.0", From 112c97a9c8ab9db8da0865e88acc7701fbe0f834 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 27 Feb 2023 23:57:18 +0000 Subject: [PATCH 20/52] Bump tox from 4.4.5 to 4.4.6 Bumps [tox](https://github.com/tox-dev/tox) from 4.4.5 to 4.4.6. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.4.5...4.4.6) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 47b3af5e..9db02ca4 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.3", "pytest-cov==4.0.0", "testfixtures==7.1.0", - "tox==4.4.5", + "tox==4.4.6", "flake8==6.0.0", "flake8-docstrings==1.7.0", "aioresponses==0.7.4", From e9ad5baea6413b07d8b808127b6694547b07c1c5 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 13 Mar 2023 23:57:15 +0000 Subject: [PATCH 21/52] Bump tox from 4.4.6 to 4.4.7 Bumps [tox](https://github.com/tox-dev/tox) from 4.4.6 to 4.4.7. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.4.6...4.4.7) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index fab8425d..0fd432af 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.3", "pytest-cov==4.0.0", "testfixtures==7.1.0", - "tox==4.4.6", + "tox==4.4.7", "flake8==6.0.0", "flake8-docstrings==1.7.0", "aioresponses==0.7.4", From eb3af9b5a17c429a65b3757612f49562831d9d02 Mon Sep 17 00:00:00 2001 From: Stefan Negru Date: Tue, 14 Mar 2023 07:52:41 +0200 Subject: [PATCH 22/52] handover link changed --- docs/optionals.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/optionals.rst b/docs/optionals.rst index 6bb8e927..d498123d 100644 --- a/docs/optionals.rst +++ b/docs/optionals.rst @@ -10,7 +10,7 @@ Handover Protocol The handover protocol is a feature comparable to `HATEOAS and HAL `_. It can be used to convey extra information regarding the Beacon service, or the dataset response. -More information about the handover protocol can be read from the `Beacon Project page `_ and +More information about the handover protocol can be read from the `Beacon Project page `_ and Beacon Specification's `handover issue `_ at Github. The handover protocol can be configured in ``config.ini`` as follows: From 7e1f3ed80f2ffaa53de936ffd05807859c1fe74e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 20 Mar 2023 07:06:14 +0000 Subject: [PATCH 23/52] Bump coverage from 7.2.1 to 7.2.2 Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.2.1 to 7.2.2. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](https://github.com/nedbat/coveragepy/compare/7.2.1...7.2.2) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 0fd432af..b5823d47 100644 --- a/setup.py +++ b/setup.py @@ -55,7 +55,7 @@ "Cython==0.29.33", ], "test": [ - "coverage==7.2.1", + "coverage==7.2.2", "pytest<7.3", "pytest-cov==4.0.0", "testfixtures==7.1.0", From 630c02bf8df17928479660656091a80135c4505e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 27 Mar 2023 06:28:05 +0000 Subject: [PATCH 24/52] Bump tox from 4.4.7 to 4.4.8 Bumps [tox](https://github.com/tox-dev/tox) from 4.4.7 to 4.4.8. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.4.7...4.4.8) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index b5823d47..4403a2fe 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.3", "pytest-cov==4.0.0", "testfixtures==7.1.0", - "tox==4.4.7", + "tox==4.4.8", "flake8==6.0.0", "flake8-docstrings==1.7.0", "aioresponses==0.7.4", From 75cdcd355697535d2e79df1cf76de43cae16b2ce Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 3 Apr 2023 13:32:14 +0000 Subject: [PATCH 25/52] Bump cython from 0.29.33 to 0.29.34 Bumps [cython](https://github.com/cython/cython) from 0.29.33 to 0.29.34. - [Release notes](https://github.com/cython/cython/releases) - [Changelog](https://github.com/cython/cython/blob/master/CHANGES.rst) - [Commits](https://github.com/cython/cython/compare/0.29.33...0.29.34) --- updated-dependencies: - dependency-name: cython dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 00c29935..d985d333 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,7 +2,7 @@ aiohttp==3.8.4 aiohttp-cors==0.7.0 asyncpg==0.27.0 jsonschema==4.17.3 -Cython==0.29.33 +Cython==0.29.34 cyvcf2==0.30.18 uvloop==0.17.0 aiocache==0.11.1 diff --git a/setup.py b/setup.py index 4403a2fe..0806bf24 100644 --- a/setup.py +++ b/setup.py @@ -52,7 +52,7 @@ "vcf": [ "numpy==1.24.2", "cyvcf2==0.30.18", - "Cython==0.29.33", + "Cython==0.29.34", ], "test": [ "coverage==7.2.2", From c7120c06bcd52fcce02a8a10ea0bd5b485690921 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 3 Apr 2023 13:32:20 +0000 Subject: [PATCH 26/52] Bump black from 23.1.0 to 23.3.0 Bumps [black](https://github.com/psf/black) from 23.1.0 to 23.3.0. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](https://github.com/psf/black/compare/23.1.0...23.3.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 4403a2fe..936de706 100644 --- a/setup.py +++ b/setup.py @@ -63,7 +63,7 @@ "flake8==6.0.0", "flake8-docstrings==1.7.0", "aioresponses==0.7.4", - "black==23.1.0", + "black==23.3.0", ], "docs": ["sphinx >= 1.4", "sphinx_rtd_theme==1.2.0"], }, From ddf454bd7452a076567aa1fc98104e7de6287b9b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 10 Apr 2023 23:56:57 +0000 Subject: [PATCH 27/52] Bump coverage from 7.2.2 to 7.2.3 Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.2.2 to 7.2.3. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](https://github.com/nedbat/coveragepy/compare/7.2.2...7.2.3) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 6b84fbdd..48ee1527 100644 --- a/setup.py +++ b/setup.py @@ -55,7 +55,7 @@ "Cython==0.29.34", ], "test": [ - "coverage==7.2.2", + "coverage==7.2.3", "pytest<7.3", "pytest-cov==4.0.0", "testfixtures==7.1.0", From 791e668d11b765503ba9a4c712125699c729dfb6 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 11 Apr 2023 00:13:50 +0000 Subject: [PATCH 28/52] Update pytest requirement from <7.3 to <7.4 Updates the requirements on [pytest](https://github.com/pytest-dev/pytest) to permit the latest version. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/1.0.0b3...7.3.0) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:development ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 48ee1527..ccd92f6c 100644 --- a/setup.py +++ b/setup.py @@ -56,7 +56,7 @@ ], "test": [ "coverage==7.2.3", - "pytest<7.3", + "pytest<7.4", "pytest-cov==4.0.0", "testfixtures==7.1.0", "tox==4.4.8", From 2935e8509c6c8d847f52b7af307eecaa808e5265 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 11 Apr 2023 00:30:34 +0000 Subject: [PATCH 29/52] Bump tox from 4.4.8 to 4.4.11 Bumps [tox](https://github.com/tox-dev/tox) from 4.4.8 to 4.4.11. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.4.8...4.4.11) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index ccd92f6c..7bbd54aa 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.4", "pytest-cov==4.0.0", "testfixtures==7.1.0", - "tox==4.4.8", + "tox==4.4.11", "flake8==6.0.0", "flake8-docstrings==1.7.0", "aioresponses==0.7.4", From eb1d6157be24d2e657443e6e899a4606ddc73185 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 17 Apr 2023 23:56:52 +0000 Subject: [PATCH 30/52] Bump dependabot/fetch-metadata from 1.3.6 to 1.4.0 Bumps [dependabot/fetch-metadata](https://github.com/dependabot/fetch-metadata) from 1.3.6 to 1.4.0. - [Release notes](https://github.com/dependabot/fetch-metadata/releases) - [Commits](https://github.com/dependabot/fetch-metadata/compare/v1.3.6...v1.4.0) --- updated-dependencies: - dependency-name: dependabot/fetch-metadata dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- .github/workflows/dependabot-auto-merge.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dependabot-auto-merge.yml b/.github/workflows/dependabot-auto-merge.yml index afa59cc6..e9443ba7 100644 --- a/.github/workflows/dependabot-auto-merge.yml +++ b/.github/workflows/dependabot-auto-merge.yml @@ -12,7 +12,7 @@ jobs: steps: - name: Dependabot metadata id: metadata - uses: dependabot/fetch-metadata@v1.3.6 + uses: dependabot/fetch-metadata@v1.4.0 with: github-token: "${{ secrets.GITHUB_TOKEN }}" - name: Wait other jobs are passed or failed From fdf499c3fbae19351547455e9dccccd24e91e615 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 17 Apr 2023 23:57:09 +0000 Subject: [PATCH 31/52] Bump tox from 4.4.11 to 4.4.12 Bumps [tox](https://github.com/tox-dev/tox) from 4.4.11 to 4.4.12. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.4.11...4.4.12) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 7bbd54aa..14d3c76c 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.4", "pytest-cov==4.0.0", "testfixtures==7.1.0", - "tox==4.4.11", + "tox==4.4.12", "flake8==6.0.0", "flake8-docstrings==1.7.0", "aioresponses==0.7.4", From 01afd20efe1b57df202fadc807b913bea3146ebd Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 24 Apr 2023 09:36:13 +0000 Subject: [PATCH 32/52] Bump numpy from 1.24.2 to 1.24.3 Bumps [numpy](https://github.com/numpy/numpy) from 1.24.2 to 1.24.3. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v1.24.2...v1.24.3) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 14d3c76c..1334dbdb 100644 --- a/setup.py +++ b/setup.py @@ -50,7 +50,7 @@ ], extras_require={ "vcf": [ - "numpy==1.24.2", + "numpy==1.24.3", "cyvcf2==0.30.18", "Cython==0.29.34", ], From dbcf1cb17b9106e288bbdf452c110cc36fee0487 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 24 Apr 2023 23:57:26 +0000 Subject: [PATCH 33/52] Bump tox from 4.4.12 to 4.5.0 Bumps [tox](https://github.com/tox-dev/tox) from 4.4.12 to 4.5.0. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.4.12...4.5.0) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 1334dbdb..9b4136ed 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.4", "pytest-cov==4.0.0", "testfixtures==7.1.0", - "tox==4.4.12", + "tox==4.5.0", "flake8==6.0.0", "flake8-docstrings==1.7.0", "aioresponses==0.7.4", From e1c401c3fd80ff6d26e57a40151fbfe0185b4116 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 1 May 2023 14:50:35 +0000 Subject: [PATCH 34/52] Bump coverage from 7.2.3 to 7.2.5 Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.2.3 to 7.2.5. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](https://github.com/nedbat/coveragepy/compare/7.2.3...7.2.5) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 9b4136ed..958414bc 100644 --- a/setup.py +++ b/setup.py @@ -55,7 +55,7 @@ "Cython==0.29.34", ], "test": [ - "coverage==7.2.3", + "coverage==7.2.5", "pytest<7.4", "pytest-cov==4.0.0", "testfixtures==7.1.0", From 0e17f0917c2ea76e74a0c74d81d5216938caf4c4 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 1 May 2023 14:50:41 +0000 Subject: [PATCH 35/52] Bump tox from 4.5.0 to 4.5.1 Bumps [tox](https://github.com/tox-dev/tox) from 4.5.0 to 4.5.1. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.5.0...4.5.1) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 9b4136ed..72b23655 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.4", "pytest-cov==4.0.0", "testfixtures==7.1.0", - "tox==4.5.0", + "tox==4.5.1", "flake8==6.0.0", "flake8-docstrings==1.7.0", "aioresponses==0.7.4", From 8570ef0107baa6c0dbb30d9b3b9ac5983c95b726 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 22 May 2023 23:56:55 +0000 Subject: [PATCH 36/52] Bump dependabot/fetch-metadata from 1.4.0 to 1.5.0 Bumps [dependabot/fetch-metadata](https://github.com/dependabot/fetch-metadata) from 1.4.0 to 1.5.0. - [Release notes](https://github.com/dependabot/fetch-metadata/releases) - [Commits](https://github.com/dependabot/fetch-metadata/compare/v1.4.0...v1.5.0) --- updated-dependencies: - dependency-name: dependabot/fetch-metadata dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- .github/workflows/dependabot-auto-merge.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dependabot-auto-merge.yml b/.github/workflows/dependabot-auto-merge.yml index e9443ba7..3237a9ea 100644 --- a/.github/workflows/dependabot-auto-merge.yml +++ b/.github/workflows/dependabot-auto-merge.yml @@ -12,7 +12,7 @@ jobs: steps: - name: Dependabot metadata id: metadata - uses: dependabot/fetch-metadata@v1.4.0 + uses: dependabot/fetch-metadata@v1.5.0 with: github-token: "${{ secrets.GITHUB_TOKEN }}" - name: Wait other jobs are passed or failed From b07550c72447dcc3dcadd2184d3b3a2e55f80b89 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 22 May 2023 23:56:58 +0000 Subject: [PATCH 37/52] Bump rojopolis/spellcheck-github-actions from 0.30.0 to 0.32.0 Bumps [rojopolis/spellcheck-github-actions](https://github.com/rojopolis/spellcheck-github-actions) from 0.30.0 to 0.32.0. - [Release notes](https://github.com/rojopolis/spellcheck-github-actions/releases) - [Changelog](https://github.com/rojopolis/spellcheck-github-actions/blob/master/CHANGELOG.md) - [Commits](https://github.com/rojopolis/spellcheck-github-actions/compare/0.30.0...0.32.0) --- updated-dependencies: - dependency-name: rojopolis/spellcheck-github-actions dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 2e6fc6e6..cb7673e3 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -13,7 +13,7 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: rojopolis/spellcheck-github-actions@0.30.0 + - uses: rojopolis/spellcheck-github-actions@0.32.0 name: Spellcheck code_docs: From ae24f4c0630a40a570849a5a53c8db96d0cbafad Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 29 May 2023 23:56:50 +0000 Subject: [PATCH 38/52] Bump dependabot/fetch-metadata from 1.5.0 to 1.5.1 Bumps [dependabot/fetch-metadata](https://github.com/dependabot/fetch-metadata) from 1.5.0 to 1.5.1. - [Release notes](https://github.com/dependabot/fetch-metadata/releases) - [Commits](https://github.com/dependabot/fetch-metadata/compare/v1.5.0...v1.5.1) --- updated-dependencies: - dependency-name: dependabot/fetch-metadata dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- .github/workflows/dependabot-auto-merge.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/dependabot-auto-merge.yml b/.github/workflows/dependabot-auto-merge.yml index 3237a9ea..842ba6bd 100644 --- a/.github/workflows/dependabot-auto-merge.yml +++ b/.github/workflows/dependabot-auto-merge.yml @@ -12,7 +12,7 @@ jobs: steps: - name: Dependabot metadata id: metadata - uses: dependabot/fetch-metadata@v1.5.0 + uses: dependabot/fetch-metadata@v1.5.1 with: github-token: "${{ secrets.GITHUB_TOKEN }}" - name: Wait other jobs are passed or failed From 521590674e576b517af0be423b0387af9406c9d6 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 29 May 2023 23:57:01 +0000 Subject: [PATCH 39/52] Bump tox from 4.5.1 to 4.5.2 Bumps [tox](https://github.com/tox-dev/tox) from 4.5.1 to 4.5.2. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.5.1...4.5.2) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index bd1da3ca..e487c7dc 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.4", "pytest-cov==4.0.0", "testfixtures==7.1.0", - "tox==4.5.1", + "tox==4.5.2", "flake8==6.0.0", "flake8-docstrings==1.7.0", "aioresponses==0.7.4", From e49bc1eb3e8038d00a760fc5d73feacab5182b26 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 29 May 2023 23:57:04 +0000 Subject: [PATCH 40/52] Bump pytest-cov from 4.0.0 to 4.1.0 Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 4.0.0 to 4.1.0. - [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest-cov/compare/v4.0.0...v4.1.0) --- updated-dependencies: - dependency-name: pytest-cov dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index bd1da3ca..c5c0e3a8 100644 --- a/setup.py +++ b/setup.py @@ -57,7 +57,7 @@ "test": [ "coverage==7.2.5", "pytest<7.4", - "pytest-cov==4.0.0", + "pytest-cov==4.1.0", "testfixtures==7.1.0", "tox==4.5.1", "flake8==6.0.0", From 4a2267998048a1854346603423a00ded2d49c137 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 29 May 2023 23:57:07 +0000 Subject: [PATCH 41/52] Bump sphinx-rtd-theme from 1.2.0 to 1.2.1 Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.2.0 to 1.2.1. - [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst) - [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/1.2.0...1.2.1) --- updated-dependencies: - dependency-name: sphinx-rtd-theme dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index bd1da3ca..b9b07704 100644 --- a/setup.py +++ b/setup.py @@ -65,6 +65,6 @@ "aioresponses==0.7.4", "black==23.3.0", ], - "docs": ["sphinx >= 1.4", "sphinx_rtd_theme==1.2.0"], + "docs": ["sphinx >= 1.4", "sphinx_rtd_theme==1.2.1"], }, ) From 78691962d5dad3bb202426312eff0926fb796751 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 29 May 2023 23:57:13 +0000 Subject: [PATCH 42/52] Bump cython from 0.29.34 to 0.29.35 Bumps [cython](https://github.com/cython/cython) from 0.29.34 to 0.29.35. - [Release notes](https://github.com/cython/cython/releases) - [Changelog](https://github.com/cython/cython/blob/master/CHANGES.rst) - [Commits](https://github.com/cython/cython/compare/0.29.34...0.29.35) --- updated-dependencies: - dependency-name: cython dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index d985d333..41d738b4 100644 --- a/requirements.txt +++ b/requirements.txt @@ -2,7 +2,7 @@ aiohttp==3.8.4 aiohttp-cors==0.7.0 asyncpg==0.27.0 jsonschema==4.17.3 -Cython==0.29.34 +Cython==0.29.35 cyvcf2==0.30.18 uvloop==0.17.0 aiocache==0.11.1 diff --git a/setup.py b/setup.py index bd1da3ca..8e73f67a 100644 --- a/setup.py +++ b/setup.py @@ -52,7 +52,7 @@ "vcf": [ "numpy==1.24.3", "cyvcf2==0.30.18", - "Cython==0.29.34", + "Cython==0.29.35", ], "test": [ "coverage==7.2.5", From 3e74eff1579dd17f84884eaddb183514a3208968 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 30 May 2023 02:21:46 +0000 Subject: [PATCH 43/52] Bump coverage from 7.2.5 to 7.2.7 Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.2.5 to 7.2.7. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](https://github.com/nedbat/coveragepy/compare/7.2.5...7.2.7) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 965ffe4b..de742c1b 100644 --- a/setup.py +++ b/setup.py @@ -55,7 +55,7 @@ "Cython==0.29.35", ], "test": [ - "coverage==7.2.5", + "coverage==7.2.7", "pytest<7.4", "pytest-cov==4.1.0", "testfixtures==7.1.0", From ae1072ed77d3628fdf99317b4e3d6c76ad9715f4 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 5 Jun 2023 23:56:50 +0000 Subject: [PATCH 44/52] Bump tox from 4.5.2 to 4.6.0 Bumps [tox](https://github.com/tox-dev/tox) from 4.5.2 to 4.6.0. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.5.2...4.6.0) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index de742c1b..9fd0c36d 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.4", "pytest-cov==4.1.0", "testfixtures==7.1.0", - "tox==4.5.2", + "tox==4.6.0", "flake8==6.0.0", "flake8-docstrings==1.7.0", "aioresponses==0.7.4", From 753250209cacdcfa124823768d9c184d5c98c988 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 12 Jun 2023 23:56:56 +0000 Subject: [PATCH 45/52] Bump sphinx-rtd-theme from 1.2.1 to 1.2.2 Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 1.2.1 to 1.2.2. - [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst) - [Commits](https://github.com/readthedocs/sphinx_rtd_theme/compare/1.2.1...1.2.2) --- updated-dependencies: - dependency-name: sphinx-rtd-theme dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 9fd0c36d..7a570411 100644 --- a/setup.py +++ b/setup.py @@ -65,6 +65,6 @@ "aioresponses==0.7.4", "black==23.3.0", ], - "docs": ["sphinx >= 1.4", "sphinx_rtd_theme==1.2.1"], + "docs": ["sphinx >= 1.4", "sphinx_rtd_theme==1.2.2"], }, ) From 0b375eff330cd6146f006cc1b145d3c2c254d622 Mon Sep 17 00:00:00 2001 From: Stefan Negru Date: Tue, 13 Jun 2023 08:29:05 +0300 Subject: [PATCH 46/52] new handovers url --- docs/optionals.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/optionals.rst b/docs/optionals.rst index d498123d..011d407e 100644 --- a/docs/optionals.rst +++ b/docs/optionals.rst @@ -10,7 +10,7 @@ Handover Protocol The handover protocol is a feature comparable to `HATEOAS and HAL `_. It can be used to convey extra information regarding the Beacon service, or the dataset response. -More information about the handover protocol can be read from the `Beacon Project page `_ and +More information about the handover protocol can be read from the `Beacon Project page `_ and Beacon Specification's `handover issue `_ at Github. The handover protocol can be configured in ``config.ini`` as follows: From df22fb7754755a26bf1957e45dc7d0f489ef808a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 13 Jun 2023 05:49:02 +0000 Subject: [PATCH 47/52] Bump ujson from 5.7.0 to 5.8.0 Bumps [ujson](https://github.com/ultrajson/ultrajson) from 5.7.0 to 5.8.0. - [Release notes](https://github.com/ultrajson/ultrajson/releases) - [Commits](https://github.com/ultrajson/ultrajson/compare/5.7.0...5.8.0) --- updated-dependencies: - dependency-name: ujson dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- requirements.txt | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 41d738b4..9e375527 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,6 +6,6 @@ Cython==0.29.35 cyvcf2==0.30.18 uvloop==0.17.0 aiocache==0.11.1 -ujson==5.7.0 +ujson==5.8.0 Authlib==1.2.0 gunicorn==20.1.0 diff --git a/setup.py b/setup.py index 7a570411..0750a886 100644 --- a/setup.py +++ b/setup.py @@ -46,7 +46,7 @@ "uvloop==0.17.0", "cyvcf2==0.30.18", "aiocache==0.11.1", - "ujson==5.7.0", + "ujson==5.8.0", ], extras_require={ "vcf": [ From a7186f607340faa1591b327114bf42a8e335d794 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 19 Jun 2023 23:57:11 +0000 Subject: [PATCH 48/52] Bump rojopolis/spellcheck-github-actions from 0.32.0 to 0.33.0 Bumps [rojopolis/spellcheck-github-actions](https://github.com/rojopolis/spellcheck-github-actions) from 0.32.0 to 0.33.0. - [Release notes](https://github.com/rojopolis/spellcheck-github-actions/releases) - [Changelog](https://github.com/rojopolis/spellcheck-github-actions/blob/master/CHANGELOG.md) - [Commits](https://github.com/rojopolis/spellcheck-github-actions/compare/0.32.0...0.33.0) --- updated-dependencies: - dependency-name: rojopolis/spellcheck-github-actions dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index cb7673e3..a1eac033 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -13,7 +13,7 @@ jobs: steps: - uses: actions/checkout@v3 - - uses: rojopolis/spellcheck-github-actions@0.32.0 + - uses: rojopolis/spellcheck-github-actions@0.33.0 name: Spellcheck code_docs: From e147a85acf8119b1a0b558c3f2b2977674ad6c27 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 19 Jun 2023 23:57:35 +0000 Subject: [PATCH 49/52] Bump tox from 4.6.0 to 4.6.2 Bumps [tox](https://github.com/tox-dev/tox) from 4.6.0 to 4.6.2. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](https://github.com/tox-dev/tox/compare/4.6.0...4.6.2) --- updated-dependencies: - dependency-name: tox dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 0750a886..5a852361 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ "pytest<7.4", "pytest-cov==4.1.0", "testfixtures==7.1.0", - "tox==4.6.0", + "tox==4.6.2", "flake8==6.0.0", "flake8-docstrings==1.7.0", "aioresponses==0.7.4", From 7672f2692c308c88890d19df652d4b40da6abf93 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 19 Jun 2023 23:57:50 +0000 Subject: [PATCH 50/52] Bump numpy from 1.24.3 to 1.25.0 Bumps [numpy](https://github.com/numpy/numpy) from 1.24.3 to 1.25.0. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](https://github.com/numpy/numpy/compare/v1.24.3...v1.25.0) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 0750a886..f55f4254 100644 --- a/setup.py +++ b/setup.py @@ -50,7 +50,7 @@ ], extras_require={ "vcf": [ - "numpy==1.24.3", + "numpy==1.25.0", "cyvcf2==0.30.18", "Cython==0.29.35", ], From 9b9c2e3e13fc8497847fd364f5232d502b15a6c2 Mon Sep 17 00:00:00 2001 From: Timo Nurminen Date: Wed, 21 Jun 2023 15:10:41 +0300 Subject: [PATCH 51/52] Update python to 3.10 --- .github/workflows/docs.yml | 2 +- .github/workflows/int.yml | 2 +- .github/workflows/style.yml | 2 +- .github/workflows/unit.yml | 4 ++-- Dockerfile | 6 +++--- README.md | 2 +- beacon_api/app.py | 4 ++-- docs/instructions.rst | 2 +- readthedocs.yml | 2 +- setup.py | 3 +-- tests/test_app.py | 2 +- tests/test_basic.py | 2 +- tox.ini | 2 +- 13 files changed, 17 insertions(+), 18 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index a1eac033..597fba5c 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -21,7 +21,7 @@ jobs: max-parallel: 4 matrix: os: [ubuntu-latest] - python-version: [3.8] + python-version: [3.10] runs-on: ${{ matrix.os }} diff --git a/.github/workflows/int.yml b/.github/workflows/int.yml index 92962db3..bbc29f06 100644 --- a/.github/workflows/int.yml +++ b/.github/workflows/int.yml @@ -9,7 +9,7 @@ jobs: max-parallel: 4 matrix: os: [ubuntu-latest] - python-version: [3.8] + python-version: [3.10] runs-on: ${{ matrix.os }} diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml index 78942b73..a8ce307f 100644 --- a/.github/workflows/style.yml +++ b/.github/workflows/style.yml @@ -8,7 +8,7 @@ jobs: max-parallel: 4 matrix: os: [ubuntu-latest] - python-version: [3.8] + python-version: [3.10] runs-on: ${{ matrix.os }} diff --git a/.github/workflows/unit.yml b/.github/workflows/unit.yml index 5ff1cb57..ffd9d081 100644 --- a/.github/workflows/unit.yml +++ b/.github/workflows/unit.yml @@ -11,7 +11,7 @@ jobs: max-parallel: 4 matrix: os: [ubuntu-latest] - python-version: [3.8] + python-version: [3.10] runs-on: ${{ matrix.os }} @@ -29,7 +29,7 @@ jobs: run: | python -m pip install --upgrade pip pip install tox tox-gh-actions coverage - - name: Run unit tests for python 3.8 + - name: Run unit tests for python 3.10 run: | tox -e unit_tests coverage lcov -o lcov.info diff --git a/Dockerfile b/Dockerfile index 0e4f4057..e54d10aa 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.8-alpine3.15 as BUILD +FROM python:3.10.12-alpine3.18 as BUILD RUN apk add --update \ && apk add --no-cache build-base curl-dev linux-headers bash git musl-dev\ @@ -18,7 +18,7 @@ COPY setup.py /root/beacon/setup.py COPY beacon_api /root/beacon/beacon_api RUN pip install /root/beacon -FROM python:3.8-alpine3.15 +FROM python:3.10.12-alpine3.18 RUN apk add --no-cache --update bash @@ -29,7 +29,7 @@ LABEL org.label-schema.vcs-url="https://github.com/CSCFI/beacon-python" RUN apk add --update \ && apk add --no-cache curl bzip2 xz -COPY --from=BUILD usr/local/lib/python3.8/ usr/local/lib/python3.8/ +COPY --from=BUILD usr/local/lib/python3.10/ usr/local/lib/python3.10/ COPY --from=BUILD /usr/local/bin/gunicorn /usr/local/bin/ diff --git a/README.md b/README.md index 2f86b872..6130dd38 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ Documentation: https://beacon-python.readthedocs.io ### Quick start `beacon-python` Web Server requires: -* Python 3.8+; +* Python 3.10+; * running DB [PostgreSQL Server](https://www.postgresql.org/) 9.6+ (recommended 13). ```shell diff --git a/beacon_api/app.py b/beacon_api/app.py index 357e5179..977448b1 100644 --- a/beacon_api/app.py +++ b/beacon_api/app.py @@ -135,7 +135,7 @@ def main(): if __name__ == "__main__": - if sys.version_info < (3, 8): - LOG.error("beacon-python requires python 3.8") + if sys.version_info < (3, 10): + LOG.error("beacon-python requires python 3.10") sys.exit(1) main() diff --git a/docs/instructions.rst b/docs/instructions.rst index 54e5f8fa..7e829c65 100644 --- a/docs/instructions.rst +++ b/docs/instructions.rst @@ -3,7 +3,7 @@ Instructions .. note:: In order to run ``beacon-python`` Web Server requirements are as specified below: - * Python 3.8+; + * Python 3.10+; * running DB `PostgreSQL Server `_ 9.6+ (recommended 13). .. _env-setup: diff --git a/readthedocs.yml b/readthedocs.yml index 1773a400..0413e75c 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -4,7 +4,7 @@ build: image: latest requirements_file: docs/docs.txt python: - version: 3.8 + version: 3.10 use_system_site_packages: true setup_py_install: true extra_requirements: diff --git a/setup.py b/setup.py index f66dfa47..2dea20f9 100644 --- a/setup.py +++ b/setup.py @@ -33,8 +33,7 @@ "Topic :: Internet :: WWW/HTTP :: HTTP Servers", "Topic :: Scientific/Engineering :: Bio-Informatics", "License :: OSI Approved :: Apache Software License", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.10", ], install_requires=[ "asyncpg==0.27.0", diff --git a/tests/test_app.py b/tests/test_app.py index 8a1f0d7d..575c51bc 100644 --- a/tests/test_app.py +++ b/tests/test_app.py @@ -5,7 +5,7 @@ import json from authlib.jose import jwt import os -from test.support import EnvironmentVarGuard +from test.support.os_helper import EnvironmentVarGuard from aiocache import caches diff --git a/tests/test_basic.py b/tests/test_basic.py index 575e9e9f..ce100aa4 100644 --- a/tests/test_basic.py +++ b/tests/test_basic.py @@ -8,7 +8,7 @@ from beacon_api.permissions.ga4gh import check_ga4gh_token, decode_passport, get_ga4gh_permissions from .test_app import PARAMS, generate_token from testfixtures import TempDirectory -from test.support import EnvironmentVarGuard +from test.support.os_helper import EnvironmentVarGuard def mock_token(bona_fide, permissions, auth): diff --git a/tox.ini b/tox.ini index 2abdedb1..e3f0069d 100644 --- a/tox.ini +++ b/tox.ini @@ -56,4 +56,4 @@ commands = py.test -x --cov=beacon_api tests/ --cov-fail-under=80 [gh-actions] python = - 3.8: flake8, unit_tests, docs, bandit, mypy + 3.10: flake8, unit_tests, docs, bandit, mypy From e3938e558957ce1b60fe0694d1e100618f8d080c Mon Sep 17 00:00:00 2001 From: Timo Nurminen Date: Wed, 21 Jun 2023 15:30:01 +0300 Subject: [PATCH 52/52] Fix workflows --- .github/workflows/docs.yml | 2 +- .github/workflows/int.yml | 2 +- .github/workflows/style.yml | 2 +- .github/workflows/unit.yml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 597fba5c..913f6970 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -21,7 +21,7 @@ jobs: max-parallel: 4 matrix: os: [ubuntu-latest] - python-version: [3.10] + python-version: ["3.10"] runs-on: ${{ matrix.os }} diff --git a/.github/workflows/int.yml b/.github/workflows/int.yml index bbc29f06..de5dc79a 100644 --- a/.github/workflows/int.yml +++ b/.github/workflows/int.yml @@ -9,7 +9,7 @@ jobs: max-parallel: 4 matrix: os: [ubuntu-latest] - python-version: [3.10] + python-version: ["3.10"] runs-on: ${{ matrix.os }} diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml index a8ce307f..3b2095f3 100644 --- a/.github/workflows/style.yml +++ b/.github/workflows/style.yml @@ -8,7 +8,7 @@ jobs: max-parallel: 4 matrix: os: [ubuntu-latest] - python-version: [3.10] + python-version: ["3.10"] runs-on: ${{ matrix.os }} diff --git a/.github/workflows/unit.yml b/.github/workflows/unit.yml index ffd9d081..a691ae58 100644 --- a/.github/workflows/unit.yml +++ b/.github/workflows/unit.yml @@ -11,7 +11,7 @@ jobs: max-parallel: 4 matrix: os: [ubuntu-latest] - python-version: [3.10] + python-version: ["3.10"] runs-on: ${{ matrix.os }}