From bceb96cb13bc956a96f397578047ec45c6196333 Mon Sep 17 00:00:00 2001 From: Gianmauro Cuccuru Date: Wed, 18 Sep 2024 21:22:58 +0200 Subject: [PATCH 01/15] stops @bruno-ariano from continuing to move the main around --- .github/workflows/test.yml | 44 +++++++++++++++++++++++++++++++++++ main.py => gwasstudio/main.py | 2 +- 2 files changed, 45 insertions(+), 1 deletion(-) create mode 100644 .github/workflows/test.yml rename main.py => gwasstudio/main.py (97%) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..ad5e1b6 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,44 @@ +name: test + +on: [push,pull_request] + +jobs: + build: + + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.10", "3.12"] + + steps: + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v2 + with: + python-version: ${{ matrix.python-version }} + + - name: cache poetry install + uses: actions/cache@v2 + with: + path: ~/.local + key: poetry-1.8.3-0 + + - name: Install poetry + run: | + python -m pip install poetry==1.8.3 + + - name: Configure poetry + run: | + python -m poetry config virtualenvs.in-project true + + - name: Cache the virtualenv + uses: actions/cache@v2 + with: + path: ./.venv + key: ${{ runner.os }}-venv-${{ hashFiles('**/poetry.lock') }} + + - name: Install dependencies + run: make dependencies + if: steps.cache-deps.outputs.cache-hit != 'true' + + - name: Install the project + run: make install diff --git a/main.py b/gwasstudio/main.py similarity index 97% rename from main.py rename to gwasstudio/main.py index 4f5ed66..cc67a52 100644 --- a/main.py +++ b/gwasstudio/main.py @@ -79,7 +79,7 @@ def cli_init( cpu_workers=cpu_workers, ).get_client() ctx.obj["client"] = client - #logger.info("Dask dashboard available at {}".format(client.get_dashboard())) + # logger.info("Dask dashboard available at {}".format(client.get_dashboard())) def main(): From 3b6fbb4b2aa6047c37277196faafcd17edc8b954 Mon Sep 17 00:00:00 2001 From: Gianmauro Cuccuru Date: Wed, 18 Sep 2024 21:26:04 +0200 Subject: [PATCH 02/15] checkout the repository --- .github/workflows/test.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index ad5e1b6..6bbc08d 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -36,6 +36,9 @@ jobs: path: ./.venv key: ${{ runner.os }}-venv-${{ hashFiles('**/poetry.lock') }} + - name: Checkout repository + uses: actions/checkout@v3 + - name: Install dependencies run: make dependencies if: steps.cache-deps.outputs.cache-hit != 'true' From 33f5256d07b73ed40c644772726ac2596c5eb9a4 Mon Sep 17 00:00:00 2001 From: Gianmauro Cuccuru Date: Wed, 18 Sep 2024 21:38:11 +0200 Subject: [PATCH 03/15] remove python 3.12 --- .github/workflows/test.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 6bbc08d..8c0cc86 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -8,7 +8,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.10", "3.12"] + python-version: ["3.10"] steps: - name: Set up Python ${{ matrix.python-version }} @@ -39,9 +39,5 @@ jobs: - name: Checkout repository uses: actions/checkout@v3 - - name: Install dependencies - run: make dependencies - if: steps.cache-deps.outputs.cache-hit != 'true' - - name: Install the project run: make install From caed5c4bcd630fb29eda506b409e898cac2f5da2 Mon Sep 17 00:00:00 2001 From: Gianmauro Cuccuru Date: Wed, 18 Sep 2024 22:03:26 +0200 Subject: [PATCH 04/15] use miniconda env --- .github/workflows/test.yml | 35 ++++++++++------------------------- environment.yml | 2 +- 2 files changed, 11 insertions(+), 26 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 8c0cc86..80a1afc 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -11,33 +11,18 @@ jobs: python-version: ["3.10"] steps: - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - - - name: cache poetry install - uses: actions/cache@v2 - with: - path: ~/.local - key: poetry-1.8.3-0 - - - name: Install poetry - run: | - python -m pip install poetry==1.8.3 - - - name: Configure poetry - run: | - python -m poetry config virtualenvs.in-project true - - - name: Cache the virtualenv - uses: actions/cache@v2 - with: - path: ./.venv - key: ${{ runner.os }}-venv-${{ hashFiles('**/poetry.lock') }} - - name: Checkout repository uses: actions/checkout@v3 + - uses: conda-incubator/setup-miniconda@v3 + with: + activate-environment: gwasstudio + environment-file: eenvironment.yml + auto-update-conda: true + python-version: ${{ matrix.python-version }} + - name: Install the project run: make install + + - name: Test version + run: gwasstudio --version diff --git a/environment.yml b/environment.yml index 28a91c2..ed21095 100644 --- a/environment.yml +++ b/environment.yml @@ -11,7 +11,7 @@ dependencies: - mamba - pip # pip must be mentioned explicitly, or conda-lock will fail - poetry=1.* # or 1.1.*, or no version at all -- as you want - - tiledb::tiledbvcf-py=0.26.* + - tiledb::tiledbvcf-py=0.35.* # Non-standard section listing target platforms for conda-lock: platforms: From 0e10f500e4a9166859c6b252e2b73f1ecc5713a7 Mon Sep 17 00:00:00 2001 From: Gianmauro Cuccuru Date: Wed, 18 Sep 2024 22:04:21 +0200 Subject: [PATCH 05/15] typo --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 80a1afc..9b04431 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -17,7 +17,7 @@ jobs: - uses: conda-incubator/setup-miniconda@v3 with: activate-environment: gwasstudio - environment-file: eenvironment.yml + environment-file: environment.yml auto-update-conda: true python-version: ${{ matrix.python-version }} From e94c8d2a1142767748f3fabeef4373971e20de64 Mon Sep 17 00:00:00 2001 From: Gianmauro Cuccuru Date: Wed, 18 Sep 2024 22:08:47 +0200 Subject: [PATCH 06/15] simplify environment.yml --- environment.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/environment.yml b/environment.yml index ed21095..adf8796 100644 --- a/environment.yml +++ b/environment.yml @@ -12,8 +12,3 @@ dependencies: - pip # pip must be mentioned explicitly, or conda-lock will fail - poetry=1.* # or 1.1.*, or no version at all -- as you want - tiledb::tiledbvcf-py=0.35.* - -# Non-standard section listing target platforms for conda-lock: -platforms: - - linux-64 - - osx-arm64 From f055ce116bdaa70e5550ad0595a243a1a1a4eefe Mon Sep 17 00:00:00 2001 From: Gianmauro Cuccuru Date: Wed, 18 Sep 2024 22:30:44 +0200 Subject: [PATCH 07/15] Update python build system --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 9b04431..c40de13 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -8,7 +8,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.10"] + python-version: ["3.11"] steps: - name: Checkout repository From 5ab9c7b089051d40174484e9a65340a8106f1e72 Mon Sep 17 00:00:00 2001 From: Gianmauro Cuccuru Date: Wed, 18 Sep 2024 22:35:02 +0200 Subject: [PATCH 08/15] Update python build system --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index adf8796..0d89f39 100644 --- a/environment.yml +++ b/environment.yml @@ -7,7 +7,7 @@ channels: # be listed explicitly here. - nodefaults dependencies: - - python=3.10.* # or don't specify the version and use the latest stable Python + - python=3.11.* # or don't specify the version and use the latest stable Python - mamba - pip # pip must be mentioned explicitly, or conda-lock will fail - poetry=1.* # or 1.1.*, or no version at all -- as you want From 54c5fcee738acaa2d675b82e3f591855acae8723 Mon Sep 17 00:00:00 2001 From: Gianmauro Cuccuru Date: Wed, 18 Sep 2024 22:39:13 +0200 Subject: [PATCH 09/15] downgrade --- .github/workflows/test.yml | 2 +- environment.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index c40de13..9b04431 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -8,7 +8,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.11"] + python-version: ["3.10"] steps: - name: Checkout repository diff --git a/environment.yml b/environment.yml index 0d89f39..d1adaf5 100644 --- a/environment.yml +++ b/environment.yml @@ -7,8 +7,8 @@ channels: # be listed explicitly here. - nodefaults dependencies: - - python=3.11.* # or don't specify the version and use the latest stable Python + - python=3.10.* # or don't specify the version and use the latest stable Python - mamba - pip # pip must be mentioned explicitly, or conda-lock will fail - poetry=1.* # or 1.1.*, or no version at all -- as you want - - tiledb::tiledbvcf-py=0.35.* + - tiledb::tiledbvcf-py=0.26.* From 0e3012fa3d280b9c497d52252b2154aee58acf7c Mon Sep 17 00:00:00 2001 From: Gianmauro Cuccuru Date: Wed, 18 Sep 2024 22:44:14 +0200 Subject: [PATCH 10/15] disable base --- .github/workflows/test.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 9b04431..08ef854 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -19,6 +19,7 @@ jobs: activate-environment: gwasstudio environment-file: environment.yml auto-update-conda: true + auto-activate-base: false python-version: ${{ matrix.python-version }} - name: Install the project From 2fd9864f620cbfa4c1ec828e4ce78185a4513eaa Mon Sep 17 00:00:00 2001 From: Gianmauro Cuccuru Date: Wed, 18 Sep 2024 22:58:13 +0200 Subject: [PATCH 11/15] not ignore bash profile files --- .github/workflows/test.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 08ef854..188b855 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -23,7 +23,9 @@ jobs: python-version: ${{ matrix.python-version }} - name: Install the project + shell: bash -el {0} run: make install - name: Test version + shell: bash -el {0} run: gwasstudio --version From e2490a4dce3229acb7a0e4be60273b1c8781a0be Mon Sep 17 00:00:00 2001 From: Gianmauro Cuccuru Date: Wed, 18 Sep 2024 23:06:25 +0200 Subject: [PATCH 12/15] add pybedtools dependency --- poetry.lock | 1444 +++++++++++++++++++++++++++--------------------- pyproject.toml | 1 + 2 files changed, 807 insertions(+), 638 deletions(-) diff --git a/poetry.lock b/poetry.lock index 2ec4cbe..4b08ba7 100755 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "annotated-types" -version = "0.6.0" +version = "0.7.0" description = "Reusable constraint types to use with typing.Annotated" optional = false python-versions = ">=3.8" files = [ - {file = "annotated_types-0.6.0-py3-none-any.whl", hash = "sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43"}, - {file = "annotated_types-0.6.0.tar.gz", hash = "sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d"}, + {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, + {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, ] [[package]] @@ -22,24 +22,39 @@ files = [ {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"}, ] +[[package]] +name = "backports-tarfile" +version = "1.2.0" +description = "Backport of CPython tarfile module" +optional = false +python-versions = ">=3.8" 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b/pyproject.toml index 9da0df8..c2034fd 100755 --- a/pyproject.toml +++ b/pyproject.toml @@ -34,6 +34,8 @@ conda-lock = "^2.3.0" scipy = "^1.14.1" numpy = "^1.26.4" pybedtools = "^0.10.0" +dask = "^2024.9.0" +dask-jobqueue = "^0.9.0" [tool.poetry.group.dev.dependencies] ruff = "^0.6.3" From 725c84b5359066ad4b72c2bbeaffc56b6b83e3d9 Mon Sep 17 00:00:00 2001 From: Gianmauro Cuccuru Date: Wed, 18 Sep 2024 23:41:42 +0200 Subject: [PATCH 15/15] update actions/checkout version --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 188b855..3fa8423 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -12,7 +12,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 - uses: conda-incubator/setup-miniconda@v3 with: