From 2cb8f4909b9d4ae0b00ffccaf561bd441b82184c Mon Sep 17 00:00:00 2001 From: John Lees Date: Tue, 13 Aug 2024 12:01:47 +0100 Subject: [PATCH 1/7] Add M1 builds for PopPUNK --- recipes/poppunk/meta.yaml | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index 802e0ca68a124..ccc67ba3a5dda 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -10,7 +10,7 @@ source: sha256: bba7cb9fad5027abc78fd6761755169ae999d3d86a96bdfbfe577a360f907067 build: - number: 0 + number: 1 skip: true # [py < 38] script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" entry_points: @@ -100,8 +100,5 @@ about: extra: identifiers: - doi:10.1101/gr.241455.118 - # enabling this would require arm64 packages for: mandrake, pp-sketchlib, - # rapidnj - # additional-platforms: - # - linux-aarch64 - # - osx-arm64 + additional-platforms: + - osx-arm64 From 7c314a119c81aac2bfd73f35647842aaae67dbad Mon Sep 17 00:00:00 2001 From: mencian Date: Tue, 20 Aug 2024 20:25:55 -0500 Subject: [PATCH 2/7] clean up recipe --- recipes/poppunk/meta.yaml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index ccc67ba3a5dda..d43fae8b33080 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -11,8 +11,8 @@ source: build: number: 1 - skip: true # [py < 38] - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv" + skip: True # [py < 38] + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" entry_points: - poppunk = PopPUNK.__main__:main - poppunk_assign = PopPUNK.assign:main @@ -27,11 +27,7 @@ build: requirements: build: - - {{ compiler('c') }} - {{ compiler('cxx') }} - - {{ compiler('fortran') }} - - llvm-openmp # [osx] - - libgomp # [linux64] - cmake >=3.18 - make host: @@ -43,6 +39,8 @@ requirements: - zlib - eigen - boost-cpp + - llvm-openmp # [osx] + - libgomp # [linux] run: # python - python @@ -64,7 +62,6 @@ requirements: - treeswift - requests # C++ extension - - zlib # The xorg-* requirements are only used for gtk3 which is pulled in via graph-tool. - xorg-libxi - xorg-libxcursor @@ -80,7 +77,6 @@ test: imports: - PopPUNK - poppunk_refine - commands: - poppunk --help - poppunk_assign --help @@ -92,13 +88,17 @@ test: - poppunk_lineages_from_strains --help about: - home: https://poppunk.bacpop.org/ - license: Apache-2.0 + home: "https://poppunk.bacpop.org" + license: "Apache-2.0" license_family: APACHE + license_file: LICENSE summary: 'PopPUNK (POPulation Partitioning Using Nucleotide Kmers)' + dev_url: "https://github.com/bacpop/PopPUNK" + doc_url: "https://poppunk.bacpop.org/index.html" extra: identifiers: - doi:10.1101/gr.241455.118 + - biotools:poppunk additional-platforms: - osx-arm64 From c06b1ce87dd11aed83a97ca895e2a03f40f22f55 Mon Sep 17 00:00:00 2001 From: mencian Date: Tue, 20 Aug 2024 20:35:49 -0500 Subject: [PATCH 3/7] clean up recipe --- recipes/poppunk/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index d43fae8b33080..1eff165a85c03 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -30,6 +30,8 @@ requirements: - {{ compiler('cxx') }} - cmake >=3.18 - make + - llvm-openmp # [osx] + - libgomp # [linux] host: # python - python @@ -39,8 +41,6 @@ requirements: - zlib - eigen - boost-cpp - - llvm-openmp # [osx] - - libgomp # [linux] run: # python - python From 5930f8c0fc93308a00f5956d24c316b68972d3c4 Mon Sep 17 00:00:00 2001 From: John Lees Date: Thu, 7 Nov 2024 11:07:52 +0000 Subject: [PATCH 4/7] Update poppunk to v2.7.1 --- recipes/poppunk/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index 1eff165a85c03..8ee00a8759b90 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.7.0" %} +{% set version = "2.7.1" %} {% set name = "PopPUNK" %} package: @@ -7,7 +7,7 @@ package: source: url: https://github.com/bacpop/{{ name|lower }}/archive/v{{ version }}.tar.gz - sha256: bba7cb9fad5027abc78fd6761755169ae999d3d86a96bdfbfe577a360f907067 + sha256: 7e6f7242b8c2150c7963fc5f4a95cfd7f2656b8a80317ff87bf97dc75f753788 build: number: 1 From cbc69b15a0c7b537b5f34757561b0f2d933a7fc2 Mon Sep 17 00:00:00 2001 From: John Lees Date: Thu, 7 Nov 2024 11:12:53 +0000 Subject: [PATCH 5/7] Reset build to zero --- recipes/poppunk/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index 8ee00a8759b90..8dceb6282c38a 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7e6f7242b8c2150c7963fc5f4a95cfd7f2656b8a80317ff87bf97dc75f753788 build: - number: 1 + number: 0 skip: True # [py < 38] script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" entry_points: From d929ce9824da8d54418d4bbc02d4881b5a716d26 Mon Sep 17 00:00:00 2001 From: John Lees Date: Thu, 7 Nov 2024 14:06:15 +0000 Subject: [PATCH 6/7] Add libfortran dep --- recipes/poppunk/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index 8dceb6282c38a..1295d54cc7b8c 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -63,6 +63,8 @@ requirements: - requests # C++ extension # The xorg-* requirements are only used for gtk3 which is pulled in via graph-tool. + - libgfortran # [linux64] + - gfortran_impl_osx-64 # [osx] - xorg-libxi - xorg-libxcursor - xorg-libxdamage From e69d5677ec4c4d69c43a1388c04f6aa5af898b39 Mon Sep 17 00:00:00 2001 From: John Lees Date: Thu, 7 Nov 2024 14:59:29 +0000 Subject: [PATCH 7/7] Add fortran compiler --- recipes/poppunk/meta.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/poppunk/meta.yaml b/recipes/poppunk/meta.yaml index 1295d54cc7b8c..b75e51baa76af 100644 --- a/recipes/poppunk/meta.yaml +++ b/recipes/poppunk/meta.yaml @@ -28,6 +28,7 @@ build: requirements: build: - {{ compiler('cxx') }} + - {{ compiler('fortran') }} - cmake >=3.18 - make - llvm-openmp # [osx] @@ -63,8 +64,6 @@ requirements: - requests # C++ extension # The xorg-* requirements are only used for gtk3 which is pulled in via graph-tool. - - libgfortran # [linux64] - - gfortran_impl_osx-64 # [osx] - xorg-libxi - xorg-libxcursor - xorg-libxdamage