From bf0a002d9a2c3796315cdb3860d5cd62d041d9f9 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Thu, 25 Apr 2024 18:12:47 +0100 Subject: [PATCH 01/26] Added pypi publication workflow --- .github/workflows/publish.yml | 51 +++++++++++++++++++++++++++++++++++ pyproject.toml | 8 +++++- 2 files changed, 58 insertions(+), 1 deletion(-) create mode 100644 .github/workflows/publish.yml diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml new file mode 100644 index 0000000..cc54cab --- /dev/null +++ b/.github/workflows/publish.yml @@ -0,0 +1,51 @@ +name: Upload Python Package + +on: + release: + types: [published] + +jobs: + build: + name: Build distribution ๐Ÿ“ฆ + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.x" + - name: Install pypa/build + run: >- + python3 -m + pip install + build + --user + - name: Build a binary wheel and a source tarball + run: python3 -m build + - name: Store the distribution packages + uses: actions/upload-artifact@v3 + with: + name: python-package-distributions + path: path: dist/ + + publish-to-pypi: + name: >- + Publish Python ๐Ÿ distribution ๐Ÿ“ฆ to PyPI + needs: + - build + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/p/mgnify-pipelines-toolkit + permissions: + id-token: write # IMPORTANT: mandatory for trusted publishing + + steps: + - name: Download all the dists + uses: actions/download-artifact@v3 + with: + name: python-package-distributions + path: dist/ + - name: Publish distribution ๐Ÿ“ฆ to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/pyproject.toml b/pyproject.toml index 546964f..d1cee9d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,6 @@ [project] name = "genomeuploader" +version = "2.0.0" readme = "README.md" authors = [ {name = "MGnify team", email = "metagenomics-help@ebi.ac.uk"}, @@ -23,9 +24,14 @@ classifiers = [ dependencies = [ "requests==2.26.0", "pandas==1.4.1", - "python-dotenv==1.0.1" + "python-dotenv==1.0.1", + "ena-webin-cli" ] +[project.urls] +Homepage = "https://github.com/EBI-Metagenomics/genome_uploader" +Issues = "https://github.com/EBI-Metagenomics/genome_uploader/issues" + [tool.pytest.ini_options] minversion = "6.0" addopts = "-ra -q" From ff223255549daea7aa94ce47d0bc4545b0cb5d81 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Thu, 25 Apr 2024 18:16:37 +0100 Subject: [PATCH 02/26] pypi publication wf debug --- .github/workflows/publish.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index cc54cab..8e0eef2 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -27,7 +27,7 @@ jobs: uses: actions/upload-artifact@v3 with: name: python-package-distributions - path: path: dist/ + path: dist/ publish-to-pypi: name: >- @@ -37,7 +37,7 @@ jobs: runs-on: ubuntu-latest environment: name: pypi - url: https://pypi.org/p/mgnify-pipelines-toolkit + url: https://pypi.org/project/genomeuploader permissions: id-token: write # IMPORTANT: mandatory for trusted publishing From 05ba8217c2cf9565a5ab292068bf8a23885c27a7 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Fri, 26 Apr 2024 11:48:13 +0100 Subject: [PATCH 03/26] add python_publish workflow --- .github/workflows/publish_python.yml | 51 ++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 .github/workflows/publish_python.yml diff --git a/.github/workflows/publish_python.yml b/.github/workflows/publish_python.yml new file mode 100644 index 0000000..8e0eef2 --- /dev/null +++ b/.github/workflows/publish_python.yml @@ -0,0 +1,51 @@ +name: Upload Python Package + +on: + release: + types: [published] + +jobs: + build: + name: Build distribution ๐Ÿ“ฆ + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.x" + - name: Install pypa/build + run: >- + python3 -m + pip install + build + --user + - name: Build a binary wheel and a source tarball + run: python3 -m build + - name: Store the distribution packages + uses: actions/upload-artifact@v3 + with: + name: python-package-distributions + path: dist/ + + publish-to-pypi: + name: >- + Publish Python ๐Ÿ distribution ๐Ÿ“ฆ to PyPI + needs: + - build + runs-on: ubuntu-latest + environment: + name: pypi + url: https://pypi.org/project/genomeuploader + permissions: + id-token: write # IMPORTANT: mandatory for trusted publishing + + steps: + - name: Download all the dists + uses: actions/download-artifact@v3 + with: + name: python-package-distributions + path: dist/ + - name: Publish distribution ๐Ÿ“ฆ to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 From 2a3a60b21771a44e1aeb327c26376bcf458c5a93 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Fri, 26 Apr 2024 12:31:59 +0100 Subject: [PATCH 04/26] publish_workflow debug --- .github/workflows/publish.yml | 51 ----------------------------------- pyproject.toml | 3 --- 2 files changed, 54 deletions(-) delete mode 100644 .github/workflows/publish.yml diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml deleted file mode 100644 index 8e0eef2..0000000 --- a/.github/workflows/publish.yml +++ /dev/null @@ -1,51 +0,0 @@ -name: Upload Python Package - -on: - release: - types: [published] - -jobs: - build: - name: Build distribution ๐Ÿ“ฆ - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v4 - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: "3.x" - - name: Install pypa/build - run: >- - python3 -m - pip install - build - --user - - name: Build a binary wheel and a source tarball - run: python3 -m build - - name: Store the distribution packages - uses: actions/upload-artifact@v3 - with: - name: python-package-distributions - path: dist/ - - publish-to-pypi: - name: >- - Publish Python ๐Ÿ distribution ๐Ÿ“ฆ to PyPI - needs: - - build - runs-on: ubuntu-latest - environment: - name: pypi - url: https://pypi.org/project/genomeuploader - permissions: - id-token: write # IMPORTANT: mandatory for trusted publishing - - steps: - - name: Download all the dists - uses: actions/download-artifact@v3 - with: - name: python-package-distributions - path: dist/ - - name: Publish distribution ๐Ÿ“ฆ to PyPI - uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/pyproject.toml b/pyproject.toml index d1cee9d..4306418 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -60,9 +60,6 @@ build-backend = "setuptools.build_meta" [tool.setuptools] packages = ["genomeuploader"] -[tool.setuptools.dynamic] -version = {attr = "genomeuploader.__version__"} - [project.scripts] genome_upload = "genomeuploader.genome_upload:main" From d439e4e56ef3d069574e4e6dcfbc44e7d03eb6f4 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Fri, 26 Apr 2024 13:01:52 +0100 Subject: [PATCH 05/26] remove version arg redundancy --- genomeuploader/__init__.py | 1 - 1 file changed, 1 deletion(-) diff --git a/genomeuploader/__init__.py b/genomeuploader/__init__.py index 8c0d5d5..e69de29 100644 --- a/genomeuploader/__init__.py +++ b/genomeuploader/__init__.py @@ -1 +0,0 @@ -__version__ = "2.0.0" From 5bd8f17cc175836021a34ac759498b217b64bb2b Mon Sep 17 00:00:00 2001 From: Ge94 Date: Mon, 29 Apr 2024 09:39:40 +0100 Subject: [PATCH 06/26] GA tests --- genomeuploader/__init__.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/genomeuploader/__init__.py b/genomeuploader/__init__.py index e69de29..7ca7aca 100644 --- a/genomeuploader/__init__.py +++ b/genomeuploader/__init__.py @@ -0,0 +1,2 @@ +from importlib.metadata import version +__version__ = version("genomeuploader") From cd3e87abb7eca84655fac7c1c727c4dffa9fd3a2 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Mon, 29 Apr 2024 09:56:15 +0100 Subject: [PATCH 07/26] GA tests --- genomeuploader/__init__.py | 3 +-- pyproject.toml | 2 -- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/genomeuploader/__init__.py b/genomeuploader/__init__.py index 7ca7aca..afced14 100644 --- a/genomeuploader/__init__.py +++ b/genomeuploader/__init__.py @@ -1,2 +1 @@ -from importlib.metadata import version -__version__ = version("genomeuploader") +__version__ = '2.0.0' diff --git a/pyproject.toml b/pyproject.toml index 4306418..3ca2b68 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,13 +1,11 @@ [project] name = "genomeuploader" -version = "2.0.0" readme = "README.md" authors = [ {name = "MGnify team", email = "metagenomics-help@ebi.ac.uk"}, ] license = {text = "Apache Software License 2.0"} keywords = ["bioinformatics", "tool", "metagenomics"] -dynamic = ["version"] description = "Python script to upload bins and MAGs in fasta format to ENA (European Nucleotide Archive). This script generates xmls and manifests necessary for submission with webin-cli." requires-python = ">=3.8" classifiers = [ From 615fa179d875c9305411cfc1a3f2d120fa679094 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Mon, 29 Apr 2024 10:04:06 +0100 Subject: [PATCH 08/26] GA tests --- pyproject.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/pyproject.toml b/pyproject.toml index 3ca2b68..7ccbdc1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,6 @@ [project] name = "genomeuploader" +version = "2.0.0" readme = "README.md" authors = [ {name = "MGnify team", email = "metagenomics-help@ebi.ac.uk"}, From c21139d1ee69f74a2dcd91a3ee0b58835e56e3e8 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Mon, 29 Apr 2024 10:05:43 +0100 Subject: [PATCH 09/26] GA tests --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 7ccbdc1..5288dc5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,7 +24,7 @@ dependencies = [ "requests==2.26.0", "pandas==1.4.1", "python-dotenv==1.0.1", - "ena-webin-cli" + "ena-webin-cli>=7.0.0" ] [project.urls] From cdd830005d22d60093531f2ffd0ccffe542fccf6 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Mon, 29 Apr 2024 10:14:43 +0100 Subject: [PATCH 10/26] GA tests --- pyproject.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 5288dc5..c166437 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,8 +23,7 @@ classifiers = [ dependencies = [ "requests==2.26.0", "pandas==1.4.1", - "python-dotenv==1.0.1", - "ena-webin-cli>=7.0.0" + "python-dotenv==1.0.1" ] [project.urls] From 30649bc5eba4771b016710d76e6af24dac3acc07 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Mon, 29 Apr 2024 10:44:51 +0100 Subject: [PATCH 11/26] publish GA test --- .github/workflows/publish_python.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/publish_python.yml b/.github/workflows/publish_python.yml index 8e0eef2..affc613 100644 --- a/.github/workflows/publish_python.yml +++ b/.github/workflows/publish_python.yml @@ -1,7 +1,7 @@ name: Upload Python Package on: - release: + push: types: [published] jobs: From ad89694b030eaf705003b340eceac4e9f55ac3e1 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Mon, 29 Apr 2024 10:59:41 +0100 Subject: [PATCH 12/26] publish_python GA test --- .github/workflows/publish_python.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/publish_python.yml b/.github/workflows/publish_python.yml index affc613..016a87f 100644 --- a/.github/workflows/publish_python.yml +++ b/.github/workflows/publish_python.yml @@ -2,7 +2,7 @@ name: Upload Python Package on: push: - types: [published] + branches: [main, feature/bioconda_package] jobs: build: From 1544e70e9e50464987421b576c5f01c9af878491 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Mon, 29 Apr 2024 11:13:26 +0100 Subject: [PATCH 13/26] Updated GAs --- .github/workflows/pytest_workflow.yml | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 .github/workflows/pytest_workflow.yml diff --git a/.github/workflows/pytest_workflow.yml b/.github/workflows/pytest_workflow.yml new file mode 100644 index 0000000..cecfa3c --- /dev/null +++ b/.github/workflows/pytest_workflow.yml @@ -0,0 +1,26 @@ +name: Run pytest + +on: + push: + branches: [main] + pull_request: + branches: [main] + +jobs: + pytest: + name: Run pytest + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v3 + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.9" + - name: Install dependencies + run: pip install .[tests] + - uses: pavelzw/pytest-action@v2 + with: + emoji: false + verbose: true + job-summary: true From f13035a15b89e73bfb427f23b9998bd36c3c9475 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Mon, 29 Apr 2024 11:32:01 +0100 Subject: [PATCH 14/26] Updated trusted publishers (pypi) --- .github/workflows/pytest_workflow.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pytest_workflow.yml b/.github/workflows/pytest_workflow.yml index cecfa3c..bdb2ea8 100644 --- a/.github/workflows/pytest_workflow.yml +++ b/.github/workflows/pytest_workflow.yml @@ -2,7 +2,7 @@ name: Run pytest on: push: - branches: [main] + branches: [main, feature/bioconda_package] pull_request: branches: [main] From 546412bbf1348575c973326e28b3dca899ec18e9 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Mon, 29 Apr 2024 15:04:00 +0100 Subject: [PATCH 15/26] changed package name for pypi --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c166437..8a798d9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,5 @@ [project] -name = "genomeuploader" +name = "genome_uploader" version = "2.0.0" readme = "README.md" authors = [ From 899b446fbd2a864b3b00dc21d3b1d9d4565e16e3 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Mon, 29 Apr 2024 15:20:34 +0100 Subject: [PATCH 16/26] Push new version for GA tests --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 8a798d9..ccfa63d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "genome_uploader" -version = "2.0.0" +version = "2.0.1" readme = "README.md" authors = [ {name = "MGnify team", email = "metagenomics-help@ebi.ac.uk"}, From 2308f0c0920ff67729bfae0573796139545b641f Mon Sep 17 00:00:00 2001 From: Ge94 Date: Mon, 29 Apr 2024 15:36:00 +0100 Subject: [PATCH 17/26] pytest_workflow testing --- .github/workflows/publish_python.yml | 4 ++-- .github/workflows/pytest_workflow.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/publish_python.yml b/.github/workflows/publish_python.yml index 016a87f..8e0eef2 100644 --- a/.github/workflows/publish_python.yml +++ b/.github/workflows/publish_python.yml @@ -1,8 +1,8 @@ name: Upload Python Package on: - push: - branches: [main, feature/bioconda_package] + release: + types: [published] jobs: build: diff --git a/.github/workflows/pytest_workflow.yml b/.github/workflows/pytest_workflow.yml index bdb2ea8..9266d49 100644 --- a/.github/workflows/pytest_workflow.yml +++ b/.github/workflows/pytest_workflow.yml @@ -18,7 +18,7 @@ jobs: with: python-version: "3.9" - name: Install dependencies - run: pip install .[tests] + run: pip install .[test] - uses: pavelzw/pytest-action@v2 with: emoji: false From aed661179d8d4b257845d25a1a143307dbd7e740 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Mon, 29 Apr 2024 15:47:36 +0100 Subject: [PATCH 18/26] pytest_workflow testing --- pyproject.toml | 4 +++- pytest.ini | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index ccfa63d..b54786d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -47,7 +47,9 @@ dev = [ "bump-my-version==0.9.2", ] test = [ - "pytest==7.1.2", + "pytest==7.4.0", + "pytest-md==0.2.0", + "pytest-workflow==2.0.1", "pytest-cov==3.0.0", ] diff --git a/pytest.ini b/pytest.ini index 0e86f06..8e78522 100644 --- a/pytest.ini +++ b/pytest.ini @@ -1,3 +1,3 @@ [pytest] python_files = tests/*.py -pythonpath = . \ No newline at end of file +testpaths = tests From 926adf7e5c4e55e93aae5bb9ec5c0c8146775432 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Tue, 30 Apr 2024 11:18:37 +0100 Subject: [PATCH 19/26] Push version to trigger GAs --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index b54786d..47e2b47 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "genome_uploader" -version = "2.0.1" +version = "2.0.2" readme = "README.md" authors = [ {name = "MGnify team", email = "metagenomics-help@ebi.ac.uk"}, From 049acc7f4ffd2cb9222fd83a8da0f77ef4e5c220 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Tue, 30 Apr 2024 11:32:42 +0100 Subject: [PATCH 20/26] Usage of GA environment --- .github/workflows/pytest_workflow.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pytest_workflow.yml b/.github/workflows/pytest_workflow.yml index 9266d49..c982336 100644 --- a/.github/workflows/pytest_workflow.yml +++ b/.github/workflows/pytest_workflow.yml @@ -10,6 +10,7 @@ jobs: pytest: name: Run pytest runs-on: ubuntu-latest + environment: pypi steps: - uses: actions/checkout@v3 From 113f1dae951da4416d8c322a6b920ec5790ccd6b Mon Sep 17 00:00:00 2001 From: Ge94 Date: Tue, 30 Apr 2024 12:28:53 +0100 Subject: [PATCH 21/26] Credentials in pytest env --- .github/workflows/pytest_workflow.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/pytest_workflow.yml b/.github/workflows/pytest_workflow.yml index c982336..88b57ce 100644 --- a/.github/workflows/pytest_workflow.yml +++ b/.github/workflows/pytest_workflow.yml @@ -11,7 +11,6 @@ jobs: name: Run pytest runs-on: ubuntu-latest environment: pypi - steps: - uses: actions/checkout@v3 - name: Set up Python @@ -21,6 +20,9 @@ jobs: - name: Install dependencies run: pip install .[test] - uses: pavelzw/pytest-action@v2 + env: + ENA_WEBIN: ${{ secrets.ENA_WEBIN }} + ENA_WEBIN_PASSWORD: ${{ secrets.ENA_WEBIN_PASSWORD }} with: emoji: false verbose: true From 082f03922bb2924bbaa5b7b1f5b4834177482ae4 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Tue, 30 Apr 2024 13:08:09 +0100 Subject: [PATCH 22/26] Credentials in all tests --- .github/workflows/test.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 05542ac..5020db8 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -20,5 +20,8 @@ jobs: run: | pip install .[test] - name: ๐Ÿงช - Testing + env: + ENA_WEBIN: ${{ secrets.ENA_WEBIN }} + ENA_WEBIN_PASSWORD: ${{ secrets.ENA_WEBIN_PASSWORD }} run: | pytest -v From 1d1114a1c1805579826735477e06a49a1ac2387b Mon Sep 17 00:00:00 2001 From: Germana Baldi Date: Tue, 30 Apr 2024 14:15:48 +0100 Subject: [PATCH 23/26] Fix credentials from env for GAs --- .github/workflows/test.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 5020db8..b5c10c1 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -8,14 +8,13 @@ jobs: strategy: matrix: python-version: [3.8, 3.9, "3.10"] - + environment: pypi steps: - uses: actions/checkout@v2 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v2 with: python-version: ${{ matrix.python-version }} - - name: Install Dependencies run: | pip install .[test] From c854f4c0e632f1ca7ed18d5a84dcf60361faae8d Mon Sep 17 00:00:00 2001 From: Germana Baldi Date: Tue, 30 Apr 2024 14:46:31 +0100 Subject: [PATCH 24/26] Run pytest in python 3.8,3.9,3.10 --- .github/workflows/pytest_workflow.yml | 50 +++++++++++++++++++++++++-- 1 file changed, 48 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pytest_workflow.yml b/.github/workflows/pytest_workflow.yml index 88b57ce..36d3545 100644 --- a/.github/workflows/pytest_workflow.yml +++ b/.github/workflows/pytest_workflow.yml @@ -7,8 +7,31 @@ on: branches: [main] jobs: - pytest: - name: Run pytest + pytest_38: + name: Run pytest 3.8 + runs-on: ubuntu-latest + environment: pypi + steps: + - uses: actions/checkout@v3 + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.8" + - name: Install dependencies + run: pip install .[test] + - uses: pavelzw/pytest-action@v2 + env: + ENA_WEBIN: ${{ secrets.ENA_WEBIN }} + ENA_WEBIN_PASSWORD: ${{ secrets.ENA_WEBIN_PASSWORD }} + with: + emoji: false + verbose: true + job-summary: true + + pytest_39: + name: Run pytest 3.9 + needs: + - pytest_38 runs-on: ubuntu-latest environment: pypi steps: @@ -27,3 +50,26 @@ jobs: emoji: false verbose: true job-summary: true + + pytest_310: + name: Run pytest 3.10 + needs: + - pytest_39 + runs-on: ubuntu-latest + environment: pypi + steps: + - uses: actions/checkout@v3 + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: "3.10" + - name: Install dependencies + run: pip install .[test] + - uses: pavelzw/pytest-action@v2 + env: + ENA_WEBIN: ${{ secrets.ENA_WEBIN }} + ENA_WEBIN_PASSWORD: ${{ secrets.ENA_WEBIN_PASSWORD }} + with: + emoji: false + verbose: true + job-summary: true From 65cf0253240a0bcf0fb124ab853b42dcdfc88213 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Tue, 30 Apr 2024 15:23:03 +0100 Subject: [PATCH 25/26] Finalised pytests, repo ready for bioconda --- .github/workflows/pytest_workflow.yml | 2 +- .github/workflows/test.yml | 26 -------------------------- pyproject.toml | 2 +- 3 files changed, 2 insertions(+), 28 deletions(-) delete mode 100644 .github/workflows/test.yml diff --git a/.github/workflows/pytest_workflow.yml b/.github/workflows/pytest_workflow.yml index 36d3545..c0b190f 100644 --- a/.github/workflows/pytest_workflow.yml +++ b/.github/workflows/pytest_workflow.yml @@ -2,7 +2,7 @@ name: Run pytest on: push: - branches: [main, feature/bioconda_package] + branches: [main] pull_request: branches: [main] diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml deleted file mode 100644 index b5c10c1..0000000 --- a/.github/workflows/test.yml +++ /dev/null @@ -1,26 +0,0 @@ -name: Testing - -on: [push, pull_request] - -jobs: - build: - runs-on: ubuntu-latest - strategy: - matrix: - python-version: [3.8, 3.9, "3.10"] - environment: pypi - steps: - - uses: actions/checkout@v2 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - - name: Install Dependencies - run: | - pip install .[test] - - name: ๐Ÿงช - Testing - env: - ENA_WEBIN: ${{ secrets.ENA_WEBIN }} - ENA_WEBIN_PASSWORD: ${{ secrets.ENA_WEBIN_PASSWORD }} - run: | - pytest -v diff --git a/pyproject.toml b/pyproject.toml index 47e2b47..1a871b3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "genome_uploader" -version = "2.0.2" +version = "2.1.0" readme = "README.md" authors = [ {name = "MGnify team", email = "metagenomics-help@ebi.ac.uk"}, From 6c6e3000d2fb026d752f8bcb3319451cdb568221 Mon Sep 17 00:00:00 2001 From: Ge94 Date: Tue, 30 Apr 2024 15:27:15 +0100 Subject: [PATCH 26/26] Fixed version --- genomeuploader/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/genomeuploader/__init__.py b/genomeuploader/__init__.py index afced14..a33997d 100644 --- a/genomeuploader/__init__.py +++ b/genomeuploader/__init__.py @@ -1 +1 @@ -__version__ = '2.0.0' +__version__ = '2.1.0'