From cdada4aa15252363db5b3a7afcffb45a91037a1b Mon Sep 17 00:00:00 2001 From: SHANG Jiayu Date: Thu, 31 Oct 2024 12:28:25 +0800 Subject: [PATCH 01/17] Update PhaBOX 2.1.2 Update PhaBOX to 2.1.2 version and add new requirements --- recipes/phabox/meta.yaml | 60 +++++++++++++++++++++++----------------- 1 file changed, 34 insertions(+), 26 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index 33d901868c12f..b3bdaef73255b 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -1,61 +1,69 @@ {% set name = "PhaBOX" %} -{% set version = "2.1.0" %} +{% set version = "2.1.2" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - url: https://github.com/KennthShang/{{ name }}/archive/refs/tags/{{ version }}.tar.gz - sha256: 0ffe4da03ccc2aac77c17866033ce513f72a5ecdf9df108abbcdbfced438b04c + url: https://github.com/KennthShang/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: d23a9d0bd68c49e8729ae893a7436f2b907e745637450b3a473c3a88762dab75 build: number: 0 noarch: python script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" entry_points: - - phabox2 = phabox2.phabox2:main - run_exports: - - {{ pin_subpackage('phabox', max_pin="x.x") }} + - phabox2=phabox2.phabox2:main requirements: host: - - pip - - python >=3.8 + - python - setuptools run: - - python >=3.8 - - biopython >=1.84 - - datasets >=3 - - kcounter >=0.1.1 - - fasttree >=2.1.11 - - mafft >=7.525 - - networkx >=3.4 - - numpy >=1.26 - - pandas >=2 - - prodigal-gv >=2.11.0 - - pyarrow >=16 - - pytorch >=2.4 - - scipy >=1.14 - - seaborn-base >=0.13.2 - - transformers >=4 + - python =3.10.14 + - diamond =0.9.14 + - blast =2.16.0 + - mcl =22.282 + - fasttree =2.1.11 + - kcounter =0.1.1 + - mafft =7.525 + - numpy =1.26.4 + - pandas =2.2.3 + - networkx =3.4.2 + - seaborn-base =0.13.2 + - biopython =1.84 + - tqdm =4.66.5 + - scipy =1.14.1 + - datasets + - transformers + - pytorch + - triton + - accelerate + - prodigal-gv test: commands: - phabox2 --help about: - home: "https://phage.ee.cityu.edu.hk" + home: https://github.com/KennthShang/PhaBOX license: "AFL-3.0" license_family: OTHER license_file: "LICENSE.md" - summary: "Phage BOX is a Python library for phage-related tasks." + summary: Virus identification and analysis tool set dev_url: "https://github.com/KennthShang/PhaBOX" doc_url: "https://github.com/KennthShang/PhaBOX/wiki" extra: recipe-maintainers: - - bernt-matthias + - SHANG Jiayu + - PENG Cheng identifiers: - doi:10.1093/bioadv/vbad101 - biotools:phabox + +channels: + - bioconda + - conda-forge + - defaults From 6aa02114a1176f97777a8e5d2239b3ca1c20fd03 Mon Sep 17 00:00:00 2001 From: SHANG Jiayu Date: Thu, 31 Oct 2024 12:35:38 +0800 Subject: [PATCH 02/17] Update meta.yaml --- recipes/phabox/meta.yaml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index b3bdaef73255b..e29f2cb0db3bc 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -62,8 +62,3 @@ extra: identifiers: - doi:10.1093/bioadv/vbad101 - biotools:phabox - -channels: - - bioconda - - conda-forge - - defaults From da332714f0e9a84a02b5024a26dc4e0070430681 Mon Sep 17 00:00:00 2001 From: SHANG Jiayu Date: Thu, 31 Oct 2024 15:47:58 +0800 Subject: [PATCH 03/17] Update meta.yaml --- recipes/phabox/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index e29f2cb0db3bc..38880f8c6e4e3 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -12,7 +12,7 @@ source: build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + script: "{{ PYTHON }} -m pip install . -vv" entry_points: - phabox2=phabox2.phabox2:main From b5be067b43116bac508016734e8422f2ce44cf59 Mon Sep 17 00:00:00 2001 From: SHANG Jiayu Date: Mon, 4 Nov 2024 17:36:01 +0800 Subject: [PATCH 04/17] Update meta.yaml --- recipes/phabox/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index 38880f8c6e4e3..07267fcaf06c5 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -1,5 +1,5 @@ {% set name = "PhaBOX" %} -{% set version = "2.1.2" %} +{% set version = "2.1.3" %} package: name: "{{ name|lower }}" @@ -7,14 +7,15 @@ package: source: url: https://github.com/KennthShang/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: d23a9d0bd68c49e8729ae893a7436f2b907e745637450b3a473c3a88762dab75 build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . -vv" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" entry_points: - phabox2=phabox2.phabox2:main + run_exports: + - {{ pin_subpackage('phabox', max_pin="x.x") }} requirements: host: From 88331636fe9b93cd05c33693914d02ad26ec81d5 Mon Sep 17 00:00:00 2001 From: SHANG Jiayu Date: Tue, 5 Nov 2024 10:22:57 +0800 Subject: [PATCH 05/17] Update meta.yaml --- recipes/phabox/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index 07267fcaf06c5..b36c52f6fd730 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -7,6 +7,7 @@ package: source: url: https://github.com/KennthShang/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz + sha256: b3e342571c7344a22913d6d2f50a2c4b44682c9de1f13a6684d08df19f8ccf36 build: number: 0 From 42d450951b1d5d814ae4e7bd5b32a0af58f1eeb8 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 5 Nov 2024 16:45:57 +0100 Subject: [PATCH 06/17] restore old pinnings --- recipes/phabox/meta.yaml | 37 +++++++++++++++++++------------------ 1 file changed, 19 insertions(+), 18 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index b36c52f6fd730..4aba9e1f3a6b3 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -20,29 +20,30 @@ build: requirements: host: - - python + - python >=3.8 + - pip - setuptools run: - - python =3.10.14 - - diamond =0.9.14 - - blast =2.16.0 - - mcl =22.282 - - fasttree =2.1.11 - - kcounter =0.1.1 - - mafft =7.525 - - numpy =1.26.4 - - pandas =2.2.3 - - networkx =3.4.2 - - seaborn-base =0.13.2 - - biopython =1.84 - - tqdm =4.66.5 - - scipy =1.14.1 + - python >=3.8 + - biopython >=1.84 - datasets - - transformers - - pytorch + - kcounter >=0.1.1 + - fasttree >=2.1.11 + - mafft >=7.525 + - networkx >=3.4 + - numpy >=1.26 + - pandas >2 + - prodigal-gv >=2.11.0 + - pytorch >=2.4 + - scipy >=1.14 + - seaborn-base >=0.13.2 + - transformers >=4 + - diamond <=0.9.14 + - blast >=2.16.0 + - mcl >=22.282 + - tqdm >=4.66.5 - triton - accelerate - - prodigal-gv test: commands: From 61ee8c6a792741e7a90275c8965dc635df46eaf8 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 5 Nov 2024 16:46:42 +0100 Subject: [PATCH 07/17] remove whitespaces --- recipes/phabox/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index 4aba9e1f3a6b3..e78c1c82d8a32 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -25,10 +25,10 @@ requirements: - setuptools run: - python >=3.8 - - biopython >=1.84 + - biopython >=1.84 - datasets - - kcounter >=0.1.1 - - fasttree >=2.1.11 + - kcounter >=0.1.1 + - fasttree >=2.1.11 - mafft >=7.525 - networkx >=3.4 - numpy >=1.26 @@ -36,10 +36,10 @@ requirements: - prodigal-gv >=2.11.0 - pytorch >=2.4 - scipy >=1.14 - - seaborn-base >=0.13.2 + - seaborn-base >=0.13.2 - transformers >=4 - diamond <=0.9.14 - - blast >=2.16.0 + - blast >=2.16.0 - mcl >=22.282 - tqdm >=4.66.5 - triton From bafcbfe5edc8a013ab27780bbfd7ff7f1e5e1e09 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 5 Nov 2024 16:47:37 +0100 Subject: [PATCH 08/17] fix pin --- recipes/phabox/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index e78c1c82d8a32..27f330e21e6d8 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -26,13 +26,13 @@ requirements: run: - python >=3.8 - biopython >=1.84 - - datasets + - datasets >=3 - kcounter >=0.1.1 - fasttree >=2.1.11 - mafft >=7.525 - networkx >=3.4 - numpy >=1.26 - - pandas >2 + - pandas >=2 - prodigal-gv >=2.11.0 - pytorch >=2.4 - scipy >=1.14 From 01e2595e58b58fab07824ff0c5c54c346070e4e1 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 5 Nov 2024 17:01:21 +0100 Subject: [PATCH 09/17] loosen pins --- recipes/phabox/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index 27f330e21e6d8..517953be4b0a8 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -25,16 +25,16 @@ requirements: - setuptools run: - python >=3.8 - - biopython >=1.84 + - biopython - datasets >=3 - kcounter >=0.1.1 - fasttree >=2.1.11 - mafft >=7.525 - - networkx >=3.4 - - numpy >=1.26 + - networkx + - numpy - pandas >=2 - prodigal-gv >=2.11.0 - - pytorch >=2.4 + - pytorch - scipy >=1.14 - seaborn-base >=0.13.2 - transformers >=4 From 3fece2306cf6c470c063dd6995bbea9f56d55b52 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 5 Nov 2024 17:14:55 +0100 Subject: [PATCH 10/17] pin numpy <2 --- recipes/phabox/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index 517953be4b0a8..437d6eb5ba964 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -31,7 +31,7 @@ requirements: - fasttree >=2.1.11 - mafft >=7.525 - networkx - - numpy + - numpy <2 - pandas >=2 - prodigal-gv >=2.11.0 - pytorch From e136a019ed2c51162f1d93599ba3e3ac613ededb Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Tue, 5 Nov 2024 17:46:50 +0100 Subject: [PATCH 11/17] repin pytorch --- recipes/phabox/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index 437d6eb5ba964..ba282b373a77d 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -34,7 +34,7 @@ requirements: - numpy <2 - pandas >=2 - prodigal-gv >=2.11.0 - - pytorch + - pytorch >=2.4 - scipy >=1.14 - seaborn-base >=0.13.2 - transformers >=4 From 12162342d8d7a0c7febe81082dd6056e578a34f3 Mon Sep 17 00:00:00 2001 From: SHANG Jiayu Date: Wed, 6 Nov 2024 09:17:08 +0800 Subject: [PATCH 12/17] Update meta.yaml --- recipes/phabox/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index ba282b373a77d..4c887c6b4795b 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -26,18 +26,18 @@ requirements: run: - python >=3.8 - biopython - - datasets >=3 + - datasets - kcounter >=0.1.1 - fasttree >=2.1.11 - mafft >=7.525 - networkx - - numpy <2 - - pandas >=2 + - numpy >=1.26.4 + - pandas >=2.2.3 - prodigal-gv >=2.11.0 - - pytorch >=2.4 + - pytorch - scipy >=1.14 - seaborn-base >=0.13.2 - - transformers >=4 + - transformers - diamond <=0.9.14 - blast >=2.16.0 - mcl >=22.282 From bd12ad51738ff2862fce8fa4a16a5aba2b212e7c Mon Sep 17 00:00:00 2001 From: SHANG Jiayu Date: Wed, 6 Nov 2024 10:31:13 +0800 Subject: [PATCH 13/17] Update meta.yaml --- recipes/phabox/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index 4c887c6b4795b..fa155a406a406 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -20,22 +20,22 @@ build: requirements: host: - - python >=3.8 + - python >=3.10.14 - pip - setuptools run: - - python >=3.8 - - biopython + - python >=3.10.14 + - biopython >=1.84 - datasets - kcounter >=0.1.1 - fasttree >=2.1.11 - mafft >=7.525 - - networkx + - networkx >=3.4.2 - numpy >=1.26.4 - pandas >=2.2.3 - prodigal-gv >=2.11.0 - pytorch - - scipy >=1.14 + - scipy >=1.14.1 - seaborn-base >=0.13.2 - transformers - diamond <=0.9.14 From 4623a9202e808ec22ebc133ef32e7c2ac71652a2 Mon Sep 17 00:00:00 2001 From: SHANG Jiayu Date: Wed, 6 Nov 2024 10:38:29 +0800 Subject: [PATCH 14/17] Update meta.yaml --- recipes/phabox/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index fa155a406a406..7fb8bff9d26a7 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -20,11 +20,11 @@ build: requirements: host: - - python >=3.10.14 + - python >=3.10 - pip - setuptools run: - - python >=3.10.14 + - python >=3.10 - biopython >=1.84 - datasets - kcounter >=0.1.1 From ba0bb48c0bce01860e142f5bbd1f3e218e194526 Mon Sep 17 00:00:00 2001 From: SHANG Jiayu Date: Wed, 6 Nov 2024 11:42:59 +0800 Subject: [PATCH 15/17] Update meta.yaml --- recipes/phabox/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index 7fb8bff9d26a7..963dcd8a3cc7a 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -1,5 +1,5 @@ {% set name = "PhaBOX" %} -{% set version = "2.1.3" %} +{% set version = "2.1.4" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/KennthShang/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: b3e342571c7344a22913d6d2f50a2c4b44682c9de1f13a6684d08df19f8ccf36 + sha256: 963d71ac1e600f5a41cd8ff22a66a34921190e7b8afe449aa5ca3fd10fabba40 build: number: 0 @@ -53,7 +53,7 @@ about: home: https://github.com/KennthShang/PhaBOX license: "AFL-3.0" license_family: OTHER - license_file: "LICENSE.md" + license_file: "LICENSE.md" summary: Virus identification and analysis tool set dev_url: "https://github.com/KennthShang/PhaBOX" doc_url: "https://github.com/KennthShang/PhaBOX/wiki" From 95b4dff33b96b8c59f17bdb010ecf941c2aa36a6 Mon Sep 17 00:00:00 2001 From: SHANG Jiayu Date: Wed, 6 Nov 2024 12:32:18 +0800 Subject: [PATCH 16/17] Update meta.yaml --- recipes/phabox/meta.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index 963dcd8a3cc7a..4d013011fbaa8 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -28,8 +28,6 @@ requirements: - biopython >=1.84 - datasets - kcounter >=0.1.1 - - fasttree >=2.1.11 - - mafft >=7.525 - networkx >=3.4.2 - numpy >=1.26.4 - pandas >=2.2.3 From 78733b8bd146955c43e565d0adf75d2cb35bbebc Mon Sep 17 00:00:00 2001 From: SHANG Jiayu Date: Wed, 6 Nov 2024 12:54:14 +0800 Subject: [PATCH 17/17] Update meta.yaml remove all independent packages --- recipes/phabox/meta.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/recipes/phabox/meta.yaml b/recipes/phabox/meta.yaml index 4d013011fbaa8..7b2311eab5f10 100644 --- a/recipes/phabox/meta.yaml +++ b/recipes/phabox/meta.yaml @@ -36,9 +36,6 @@ requirements: - scipy >=1.14.1 - seaborn-base >=0.13.2 - transformers - - diamond <=0.9.14 - - blast >=2.16.0 - - mcl >=22.282 - tqdm >=4.66.5 - triton - accelerate