From 410aef621b0d772ea786c816f430c50b5f755f69 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Tue, 15 Oct 2024 21:06:10 -0700 Subject: [PATCH 1/9] Add pyhmmsearch --- recipes/pyhmmsearch/meta.yaml | 43 +++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 recipes/pyhmmsearch/meta.yaml diff --git a/recipes/pyhmmsearch/meta.yaml b/recipes/pyhmmsearch/meta.yaml new file mode 100644 index 0000000000000..71d6ea848a5c3 --- /dev/null +++ b/recipes/pyhmmsearch/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "pyhmmsearch" %} +{% set version = "2024.7.29" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/pyhmmsearch-{{ version }}.tar.gz + sha256: 5134759a9053a9c3f52ab6c3d672094915292d431f734074d1d33021138c75ec + +build: + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + entry_points: + - pyhmmsearch.py=pyhmmsearch/pyhmmsearch.py + - reformat_pyhmmsearch.py=reformat_pyhmmsearch.py + - serialize_hmm_models.py=serialize_hmm_models.py + run_exports: + - {{ pin_subpackage("pyhmmsearch", max_pin="x.x") }} + + +requirements: + host: + - python + - pip + run: + - python + - pyhmmer >=0.10.12 + - pandas + - tqdm + +test: + commands: + - pyhmmsearch.py -h + - reformat_pyhmmsearch.py -h + - serialize_hmm_models.py -h + +about: + home: https://github.com/new-atlantis-labs/pyhmmsearch-stable + summary: Fast implementation of HMMSEARCH optimized for high-memory systems using PyHmmer + license: MIT + license_file: LICENSE \ No newline at end of file From d50a150c3d65c7f8dc41bc29e066c2926d2fe9e9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Tue, 15 Oct 2024 21:19:19 -0700 Subject: [PATCH 2/9] Add noarch --- recipes/pyhmmsearch/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/pyhmmsearch/meta.yaml b/recipes/pyhmmsearch/meta.yaml index 71d6ea848a5c3..55c68bcf39891 100644 --- a/recipes/pyhmmsearch/meta.yaml +++ b/recipes/pyhmmsearch/meta.yaml @@ -12,6 +12,7 @@ source: build: script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation number: 0 + noarch: python entry_points: - pyhmmsearch.py=pyhmmsearch/pyhmmsearch.py - reformat_pyhmmsearch.py=reformat_pyhmmsearch.py From 5a693160ef2ed6113b3d1b1cc58e87f0da89c6a5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Tue, 15 Oct 2024 21:37:27 -0700 Subject: [PATCH 3/9] Change entrypoints --- recipes/pyhmmsearch/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pyhmmsearch/meta.yaml b/recipes/pyhmmsearch/meta.yaml index 55c68bcf39891..8738b899f56f8 100644 --- a/recipes/pyhmmsearch/meta.yaml +++ b/recipes/pyhmmsearch/meta.yaml @@ -14,9 +14,9 @@ build: number: 0 noarch: python entry_points: - - pyhmmsearch.py=pyhmmsearch/pyhmmsearch.py - - reformat_pyhmmsearch.py=reformat_pyhmmsearch.py - - serialize_hmm_models.py=serialize_hmm_models.py + - pyhmmsearch.py="pyhmmsearch/pyhmmsearch.py" + - reformat_pyhmmsearch.py="reformat_pyhmmsearch.py" + - serialize_hmm_models.py="serialize_hmm_models.py" run_exports: - {{ pin_subpackage("pyhmmsearch", max_pin="x.x") }} From 4498d704ab401aa1b4511e6979e63458cc562b26 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Tue, 15 Oct 2024 21:57:34 -0700 Subject: [PATCH 4/9] Change entrypoints --- recipes/pyhmmsearch/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pyhmmsearch/meta.yaml b/recipes/pyhmmsearch/meta.yaml index 8738b899f56f8..8426fcd41942a 100644 --- a/recipes/pyhmmsearch/meta.yaml +++ b/recipes/pyhmmsearch/meta.yaml @@ -14,9 +14,9 @@ build: number: 0 noarch: python entry_points: - - pyhmmsearch.py="pyhmmsearch/pyhmmsearch.py" - - reformat_pyhmmsearch.py="reformat_pyhmmsearch.py" - - serialize_hmm_models.py="serialize_hmm_models.py" + - pyhmmsearch.py=pyhmmsearch.pyhmmsearch:main + - reformat_pyhmmsearch.py=pyhmmsearch.reformat_pyhmmsearch:main + - serialize_hmm_models.py=pyhmmsearch.serialize_hmm_models:main run_exports: - {{ pin_subpackage("pyhmmsearch", max_pin="x.x") }} From 306ba88469cb7cf21a28a3cc6fa6e96e7c1c5132 Mon Sep 17 00:00:00 2001 From: mencian Date: Wed, 16 Oct 2024 00:04:59 -0500 Subject: [PATCH 5/9] edit run_exports --- recipes/pyhmmsearch/meta.yaml | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/pyhmmsearch/meta.yaml b/recipes/pyhmmsearch/meta.yaml index 8426fcd41942a..e460e403cc51a 100644 --- a/recipes/pyhmmsearch/meta.yaml +++ b/recipes/pyhmmsearch/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 5134759a9053a9c3f52ab6c3d672094915292d431f734074d1d33021138c75ec build: - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir number: 0 noarch: python entry_points: @@ -18,7 +18,7 @@ build: - reformat_pyhmmsearch.py=pyhmmsearch.reformat_pyhmmsearch:main - serialize_hmm_models.py=pyhmmsearch.serialize_hmm_models:main run_exports: - - {{ pin_subpackage("pyhmmsearch", max_pin="x.x") }} + - {{ pin_subpackage("pyhmmsearch", max_pin=None) }} requirements: @@ -38,7 +38,10 @@ test: - serialize_hmm_models.py -h about: - home: https://github.com/new-atlantis-labs/pyhmmsearch-stable - summary: Fast implementation of HMMSEARCH optimized for high-memory systems using PyHmmer + home: "https://github.com/new-atlantis-labs/pyhmmsearch-stable" + summary: "Fast implementation of HMMSEARCH optimized for high-memory systems using PyHmmer." license: MIT - license_file: LICENSE \ No newline at end of file + license_family: MIT + license_file: LICENSE + dev_url: "https://github.com/new-atlantis-labs/pyhmmsearch-stable" + doc_url: "https://github.com/new-atlantis-labs/pyhmmsearch-stable/blob/main/README.md" From d1d836d4d0d2ba681d3205949e355d1d925f6765 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Tue, 15 Oct 2024 23:24:26 -0700 Subject: [PATCH 6/9] Change entrypoints --- recipes/pyhmmsearch/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pyhmmsearch/meta.yaml b/recipes/pyhmmsearch/meta.yaml index e460e403cc51a..3aba7a419946a 100644 --- a/recipes/pyhmmsearch/meta.yaml +++ b/recipes/pyhmmsearch/meta.yaml @@ -14,9 +14,9 @@ build: number: 0 noarch: python entry_points: - - pyhmmsearch.py=pyhmmsearch.pyhmmsearch:main - - reformat_pyhmmsearch.py=pyhmmsearch.reformat_pyhmmsearch:main - - serialize_hmm_models.py=pyhmmsearch.serialize_hmm_models:main + - pyhmmsearch.py=pyhmmsearch:main + - reformat_pyhmmsearch.py=reformat_pyhmmsearch:main + - serialize_hmm_models.py=serialize_hmm_models:main run_exports: - {{ pin_subpackage("pyhmmsearch", max_pin=None) }} From 63e7ca78d95da0caccf4d8b3a398090ba22f180e Mon Sep 17 00:00:00 2001 From: mencian Date: Wed, 16 Oct 2024 18:21:09 -0500 Subject: [PATCH 7/9] try just import tests --- recipes/pyhmmsearch/meta.yaml | 17 +++++++++-------- {sopa => recipes/sopa}/meta.yaml | 10 ++++------ 2 files changed, 13 insertions(+), 14 deletions(-) rename {sopa => recipes/sopa}/meta.yaml (85%) diff --git a/recipes/pyhmmsearch/meta.yaml b/recipes/pyhmmsearch/meta.yaml index 3aba7a419946a..932b8c184e120 100644 --- a/recipes/pyhmmsearch/meta.yaml +++ b/recipes/pyhmmsearch/meta.yaml @@ -13,14 +13,13 @@ build: script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir number: 0 noarch: python - entry_points: - - pyhmmsearch.py=pyhmmsearch:main - - reformat_pyhmmsearch.py=reformat_pyhmmsearch:main - - serialize_hmm_models.py=serialize_hmm_models:main + #entry_points: + #- pyhmmsearch.py=pyhmmsearch:main + #- reformat_pyhmmsearch.py=reformat_pyhmmsearch:main + #- serialize_hmm_models.py=serialize_hmm_models:main run_exports: - {{ pin_subpackage("pyhmmsearch", max_pin=None) }} - requirements: host: - python @@ -32,10 +31,12 @@ requirements: - tqdm test: + imports: + - pyhmmsearch commands: - - pyhmmsearch.py -h - - reformat_pyhmmsearch.py -h - - serialize_hmm_models.py -h + #- pyhmmsearch.py -h + #- reformat_pyhmmsearch.py -h + #- serialize_hmm_models.py -h about: home: "https://github.com/new-atlantis-labs/pyhmmsearch-stable" diff --git a/sopa/meta.yaml b/recipes/sopa/meta.yaml similarity index 85% rename from sopa/meta.yaml rename to recipes/sopa/meta.yaml index cbe346742649b..8a23cc317640b 100644 --- a/sopa/meta.yaml +++ b/recipes/sopa/meta.yaml @@ -13,7 +13,7 @@ build: entry_points: - sopa = sopa.main:app noarch: python - script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir number: 0 requirements: @@ -37,7 +37,7 @@ requirements: - toml >=0.10.2 - loompy >=3.0.7 - tangram-sc >=1.0.4 - - snakemake >=7.32.4,<8.0.0,<8.1.3 + - snakemake-minimal >=7.32.4,<8.0.0,<8.1.3 - pulp >=2.3.1,<3.0.0,<2.8 - tiffslide >=2.3.1,<3.0.0 - black >=22.8.0,<23.0.0 @@ -54,16 +54,14 @@ test: imports: - sopa commands: - - pip check - sopa --help - requires: - - pip about: home: https://gustaveroussy.github.io/sopa - summary: Spatial-omics pipeline and analysis + summary: "Spatial-omics pipeline and analysis." license: BSD-3-Clause license_file: LICENSE + dev_url: https://gustaveroussy.github.io/sopa extra: recipe-maintainers: From be3b62d53077c3acbf0fdbf6735e40595ac3001d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Fri, 18 Oct 2024 14:29:32 -0700 Subject: [PATCH 8/9] Update version --- recipes/pyhmmsearch/meta.yaml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/recipes/pyhmmsearch/meta.yaml b/recipes/pyhmmsearch/meta.yaml index 932b8c184e120..72594487acb1d 100644 --- a/recipes/pyhmmsearch/meta.yaml +++ b/recipes/pyhmmsearch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyhmmsearch" %} -{% set version = "2024.7.29" %} +{% set version = "2024.10.18" %} package: name: {{ name|lower }} @@ -7,16 +7,16 @@ package: source: url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/pyhmmsearch-{{ version }}.tar.gz - sha256: 5134759a9053a9c3f52ab6c3d672094915292d431f734074d1d33021138c75ec + sha256: 50c150659a45934b5b69a0459038bb1c304612951c67bd046eb72e5102b29692 build: script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir number: 0 noarch: python - #entry_points: - #- pyhmmsearch.py=pyhmmsearch:main - #- reformat_pyhmmsearch.py=reformat_pyhmmsearch:main - #- serialize_hmm_models.py=serialize_hmm_models:main + entry_points: + - pyhmmsearch=pyhmmsearch.pyhmmsearch:main + - reformat_pyhmmsearch=pyhmmsearch.reformat_pyhmmsearch:main + - serialize_hmm_models=pyhmmsearch.serialize_hmm_models:main run_exports: - {{ pin_subpackage("pyhmmsearch", max_pin=None) }} @@ -34,9 +34,9 @@ test: imports: - pyhmmsearch commands: - #- pyhmmsearch.py -h - #- reformat_pyhmmsearch.py -h - #- serialize_hmm_models.py -h + - pyhmmsearch --help + - reformat_pyhmmsearch --help + - serialize_hmm_models --help about: home: "https://github.com/new-atlantis-labs/pyhmmsearch-stable" From 2ec368e550c87efd9f59cd3341f9f0ffee72eae8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Fri, 18 Oct 2024 15:53:43 -0700 Subject: [PATCH 9/9] Add version constraints --- recipes/pyhmmsearch/meta.yaml | 4 ++-- recipes/sopa/meta.yaml | 10 ++++++---- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/pyhmmsearch/meta.yaml b/recipes/pyhmmsearch/meta.yaml index 72594487acb1d..4e962d96fb235 100644 --- a/recipes/pyhmmsearch/meta.yaml +++ b/recipes/pyhmmsearch/meta.yaml @@ -27,8 +27,8 @@ requirements: run: - python - pyhmmer >=0.10.12 - - pandas - - tqdm + - pandas >= 2 + - tqdm >= 4 test: imports: diff --git a/recipes/sopa/meta.yaml b/recipes/sopa/meta.yaml index 8a23cc317640b..cbe346742649b 100644 --- a/recipes/sopa/meta.yaml +++ b/recipes/sopa/meta.yaml @@ -13,7 +13,7 @@ build: entry_points: - sopa = sopa.main:app noarch: python - script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation number: 0 requirements: @@ -37,7 +37,7 @@ requirements: - toml >=0.10.2 - loompy >=3.0.7 - tangram-sc >=1.0.4 - - snakemake-minimal >=7.32.4,<8.0.0,<8.1.3 + - snakemake >=7.32.4,<8.0.0,<8.1.3 - pulp >=2.3.1,<3.0.0,<2.8 - tiffslide >=2.3.1,<3.0.0 - black >=22.8.0,<23.0.0 @@ -54,14 +54,16 @@ test: imports: - sopa commands: + - pip check - sopa --help + requires: + - pip about: home: https://gustaveroussy.github.io/sopa - summary: "Spatial-omics pipeline and analysis." + summary: Spatial-omics pipeline and analysis license: BSD-3-Clause license_file: LICENSE - dev_url: https://gustaveroussy.github.io/sopa extra: recipe-maintainers: