From 7ceae2dabf5e08d1bdc3e8f07c6356c0b51aea9a Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 3 Sep 2018 16:10:54 +0100 Subject: [PATCH 01/10] Bump version --- recipes/r-workflowscriptscommon/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-workflowscriptscommon/meta.yaml b/recipes/r-workflowscriptscommon/meta.yaml index dd5cad66295e5..27bb666319959 100644 --- a/recipes/r-workflowscriptscommon/meta.yaml +++ b/recipes/r-workflowscriptscommon/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.0.1' %} +{% set version = '0.0.2' %} package: name: r-workflowscriptscommon @@ -6,7 +6,7 @@ package: source: url: https://github.com/ebi-gene-expression-group/workflowscriptscommon/archive/v{{ version }}.tar.gz - sha256: abab299f7ff1c752e52d09cf5ee6260b3320fb8fcb6df3ee7a5e7413e30a5870 + sha256: bf4aeb7fab3c58b245f21c25548e072756ac03bc7ce7bbb6bf7eb5dc85a6c01e build: number: 0 From a1a9fcb056a688bcc2ba7819c991622e715234ba Mon Sep 17 00:00:00 2001 From: nh3 Date: Fri, 19 Oct 2018 10:26:06 +0100 Subject: [PATCH 02/10] First implementation of scanpy-scripts bioconda recipe. --- recipes/scanpy-scripts/build.sh | 5 ++++ recipes/scanpy-scripts/meta.yaml | 44 ++++++++++++++++++++++++++++++++ 2 files changed, 49 insertions(+) create mode 100644 recipes/scanpy-scripts/build.sh create mode 100644 recipes/scanpy-scripts/meta.yaml diff --git a/recipes/scanpy-scripts/build.sh b/recipes/scanpy-scripts/build.sh new file mode 100644 index 0000000000000..ecb11795f837b --- /dev/null +++ b/recipes/scanpy-scripts/build.sh @@ -0,0 +1,5 @@ +#!/usr/bin/env bash + +mkdir -p $PREFIX/bin +cp bin/*.py $PREFIX/bin +cp *.sh $PREFIX/bin diff --git a/recipes/scanpy-scripts/meta.yaml b/recipes/scanpy-scripts/meta.yaml new file mode 100644 index 0000000000000..c13d07699c424 --- /dev/null +++ b/recipes/scanpy-scripts/meta.yaml @@ -0,0 +1,44 @@ +{% set version = '0.0.1' %} + +package: + name: scanpy-scripts + version: {{ version }} + +source: + url: https://github.com/ebi-gene-expression-group/scanpy-scripts/archive/v{{ version }}.tar.gz + sha256: 2d20178efaeda632a36cf082d6ab8d64f833df983953aac2cd072673187189ed + +build: + number: 0 + noarch: generic + +requirements: + run: + - python>=3.6 + - scanpy>=1.3.2 + +test: + commands: + - scanpy-read-10x.py --help + - scanpy-filter-cells.py --help + - scanpy-filter-genes.py --help + - scanpy-normalise-data.py --help + - scanpy-find-variable-genes.py --help + - scanpy-scale-data.py --help + - scanpy-run-pca.py --help + - scanpy-neighbours.py --help + - scanpy-run-umap.py --help + - scanpy-run-tsne.py --help + - scanpy-find-cluster.py --help + - scanpy-find-markers.py --help + - which scanpy-scripts-post-install-tests.sh + +about: + home: https://github.com/ebi-gene-expression-group/scanpy-scripts + dev_url: https://github.com/ebi-gene-expression-group/scanpy-scripts + license: GPL-3 + summary: A set of wrappers for individual components of the scanpy package. + Functions in python packages are hard to call when building workflows + outside of python, so this package adds a set of simple wrappers with + robust argument parsing. + license_family: GPL From 5202d60b5a750df2de9a7cba674d7f28cbb0812b Mon Sep 17 00:00:00 2001 From: nh3 Date: Fri, 19 Oct 2018 10:35:20 +0100 Subject: [PATCH 03/10] fix path in build.sh --- recipes/scanpy-scripts/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/scanpy-scripts/build.sh b/recipes/scanpy-scripts/build.sh index ecb11795f837b..6cf47a0224eba 100644 --- a/recipes/scanpy-scripts/build.sh +++ b/recipes/scanpy-scripts/build.sh @@ -1,5 +1,5 @@ #!/usr/bin/env bash mkdir -p $PREFIX/bin -cp bin/*.py $PREFIX/bin +cp *.py $PREFIX/bin cp *.sh $PREFIX/bin From 02d9e08b64b5239712fd1e3b1824f70afae8bebb Mon Sep 17 00:00:00 2001 From: nh3 Date: Fri, 19 Oct 2018 10:58:50 +0100 Subject: [PATCH 04/10] Remove "noarch" flag as requested by bioconda recipe checklist --- recipes/scanpy-scripts/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/scanpy-scripts/meta.yaml b/recipes/scanpy-scripts/meta.yaml index c13d07699c424..a226c2f7115e6 100644 --- a/recipes/scanpy-scripts/meta.yaml +++ b/recipes/scanpy-scripts/meta.yaml @@ -10,7 +10,6 @@ source: build: number: 0 - noarch: generic requirements: run: From 0b194c344d49a45a03fd60478bca202528a3a2ac Mon Sep 17 00:00:00 2001 From: nh3 Date: Fri, 19 Oct 2018 11:00:09 +0100 Subject: [PATCH 05/10] Add a post install notice that post install test needs bats-core. --- recipes/scanpy-scripts/post-link.sh | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 recipes/scanpy-scripts/post-link.sh diff --git a/recipes/scanpy-scripts/post-link.sh b/recipes/scanpy-scripts/post-link.sh new file mode 100644 index 0000000000000..a689d8ad9d1db --- /dev/null +++ b/recipes/scanpy-scripts/post-link.sh @@ -0,0 +1,4 @@ +#!/usr/bin/env bash + +echo 'Post install test script "scanpy-scripts-post-install-tests.sh" requires' +echo 'conda package "bats-core".' From ad88fe8f18f9cf0e53c3a51f6d23f7215a348d4d Mon Sep 17 00:00:00 2001 From: nh3 Date: Fri, 19 Oct 2018 20:36:21 +0100 Subject: [PATCH 06/10] Add more dependencies --- recipes/scanpy-scripts/meta.yaml | 54 ++++++++++++++++++-------------- 1 file changed, 31 insertions(+), 23 deletions(-) diff --git a/recipes/scanpy-scripts/meta.yaml b/recipes/scanpy-scripts/meta.yaml index a226c2f7115e6..8bec87852aff6 100644 --- a/recipes/scanpy-scripts/meta.yaml +++ b/recipes/scanpy-scripts/meta.yaml @@ -10,34 +10,42 @@ source: build: number: 0 + noarch: generic requirements: + host: + - python + - setuptools run: - - python>=3.6 - - scanpy>=1.3.2 + - python>=3.6 + - setuptools + - numpy>=1.15 + - pandas>=0.23 + - matplotlib>=3.0.0 + - scanpy>=1.3.2 test: commands: - - scanpy-read-10x.py --help - - scanpy-filter-cells.py --help - - scanpy-filter-genes.py --help - - scanpy-normalise-data.py --help - - scanpy-find-variable-genes.py --help - - scanpy-scale-data.py --help - - scanpy-run-pca.py --help - - scanpy-neighbours.py --help - - scanpy-run-umap.py --help - - scanpy-run-tsne.py --help - - scanpy-find-cluster.py --help - - scanpy-find-markers.py --help - - which scanpy-scripts-post-install-tests.sh + - scanpy-read-10x.py --help + - scanpy-filter-cells.py --help + - scanpy-filter-genes.py --help + - scanpy-normalise-data.py --help + - scanpy-find-variable-genes.py --help + - scanpy-scale-data.py --help + - scanpy-run-pca.py --help + - scanpy-neighbours.py --help + - scanpy-run-umap.py --help + - scanpy-run-tsne.py --help + - scanpy-find-cluster.py --help + - scanpy-find-markers.py --help + - which scanpy-scripts-post-install-tests.sh about: - home: https://github.com/ebi-gene-expression-group/scanpy-scripts - dev_url: https://github.com/ebi-gene-expression-group/scanpy-scripts - license: GPL-3 - summary: A set of wrappers for individual components of the scanpy package. - Functions in python packages are hard to call when building workflows - outside of python, so this package adds a set of simple wrappers with - robust argument parsing. - license_family: GPL + home: https://github.com/ebi-gene-expression-group/scanpy-scripts + dev_url: https://github.com/ebi-gene-expression-group/scanpy-scripts + license: GPL-3 + summary: A set of wrappers for individual components of the scanpy package. + Functions in python packages are hard to call when building workflows + outside of python, so this package adds a set of simple wrappers with + robust argument parsing. + license_family: GPL From e106a535b50d5513742c3b63f729559832c37543 Mon Sep 17 00:00:00 2001 From: nh3 Date: Fri, 19 Oct 2018 20:57:04 +0100 Subject: [PATCH 07/10] Skip building for python versions other than 3.6 --- recipes/scanpy-scripts/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/scanpy-scripts/meta.yaml b/recipes/scanpy-scripts/meta.yaml index 8bec87852aff6..a787dd8143188 100644 --- a/recipes/scanpy-scripts/meta.yaml +++ b/recipes/scanpy-scripts/meta.yaml @@ -10,7 +10,7 @@ source: build: number: 0 - noarch: generic + skip: True # [not py36] requirements: host: From 9d1551bc81841fd2e0c1199d0745273327ce8935 Mon Sep 17 00:00:00 2001 From: nh3 Date: Mon, 22 Oct 2018 10:43:52 +0100 Subject: [PATCH 08/10] Target v0.0.2 which has non-ascii characters removed --- recipes/scanpy-scripts/meta.yaml | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/recipes/scanpy-scripts/meta.yaml b/recipes/scanpy-scripts/meta.yaml index a787dd8143188..93c642c65fc5f 100644 --- a/recipes/scanpy-scripts/meta.yaml +++ b/recipes/scanpy-scripts/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '0.0.1' %} +{% set version = '0.0.2' %} package: name: scanpy-scripts @@ -6,7 +6,7 @@ package: source: url: https://github.com/ebi-gene-expression-group/scanpy-scripts/archive/v{{ version }}.tar.gz - sha256: 2d20178efaeda632a36cf082d6ab8d64f833df983953aac2cd072673187189ed + sha256: 4d9d3193857e5f801540236db547aa91db6c1db47c43943915f130c4fa8a31b2 build: number: 0 @@ -14,13 +14,10 @@ build: requirements: host: - - python - - setuptools + - python>=3.6 run: - python>=3.6 - - setuptools - - numpy>=1.15 - - pandas>=0.23 + - pandas>=0.22 - matplotlib>=3.0.0 - scanpy>=1.3.2 From 60f85db957a699795ef27f183386cea66ed1c5a5 Mon Sep 17 00:00:00 2001 From: nh3 Date: Tue, 23 Oct 2018 11:10:24 +0100 Subject: [PATCH 09/10] Lower version requirement for pandas and matplotlib to be the same as scanpy --- recipes/scanpy-scripts/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/scanpy-scripts/meta.yaml b/recipes/scanpy-scripts/meta.yaml index 93c642c65fc5f..c9041234fd433 100644 --- a/recipes/scanpy-scripts/meta.yaml +++ b/recipes/scanpy-scripts/meta.yaml @@ -17,8 +17,8 @@ requirements: - python>=3.6 run: - python>=3.6 - - pandas>=0.22 - - matplotlib>=3.0.0 + - pandas>=0.21 + - matplotlib>=2.2.0 - scanpy>=1.3.2 test: From efe0cf1aa5edbf8ecc69b92feb48f557e32237ab Mon Sep 17 00:00:00 2001 From: nh3 Date: Tue, 23 Oct 2018 11:35:36 +0100 Subject: [PATCH 10/10] Requirement matplotlib>=3.0.0, declare noarch --- recipes/scanpy-scripts/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/scanpy-scripts/meta.yaml b/recipes/scanpy-scripts/meta.yaml index c9041234fd433..985f849167008 100644 --- a/recipes/scanpy-scripts/meta.yaml +++ b/recipes/scanpy-scripts/meta.yaml @@ -10,7 +10,7 @@ source: build: number: 0 - skip: True # [not py36] + noarch: generic requirements: host: @@ -18,7 +18,7 @@ requirements: run: - python>=3.6 - pandas>=0.21 - - matplotlib>=2.2.0 + - matplotlib>=3.0.0 - scanpy>=1.3.2 test: