From 15cf5e00dfddda1bddeb46532d2a7c6056efda07 Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Thu, 13 Apr 2023 11:11:33 +0200 Subject: [PATCH 01/13] Enable Python bindings; add license. --- recipes/illumina-interop/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index 6417abb1d19e2..7dcb87b9159b4 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -6,7 +6,7 @@ package: version: '{{version}}' build: - number: 0 + number: 1 skip: true # [osx] run_exports: - {{ pin_subpackage('illumina-interop', max_pin="x.x") }} @@ -21,8 +21,11 @@ requirements: - cmake - {{ compiler('c') }} - {{ compiler('cxx') }} + - python test: + imports: + - interop commands: - interop_dumptext | grep Version > /dev/null - interop_imaging_table | grep Version > /dev/null @@ -47,3 +50,4 @@ about: faster display of a subset of the original data (collapsed quality scores). dev_url: https://github.com/Illumina/interop license_family: GPL + license_file: LICENSE From 51bcfa5f67b9b138367520e2411eca0fd93c488b Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Wed, 20 Mar 2024 12:32:10 +0100 Subject: [PATCH 02/13] WIP: Require Python for tests --- recipes/illumina-interop/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index 7dcb87b9159b4..decfa72446edb 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -24,6 +24,8 @@ requirements: - python test: + requires: + - python imports: - interop commands: From 7654f038162555e883f739c66664d5da71120383 Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Wed, 20 Mar 2024 13:35:08 +0100 Subject: [PATCH 03/13] Add more requirements --- recipes/illumina-interop/meta.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index decfa72446edb..b0d7194f5f722 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -22,10 +22,13 @@ requirements: - {{ compiler('c') }} - {{ compiler('cxx') }} - python + - numpy + - swig test: requires: - python + - numpy imports: - interop commands: From 116611af4a2c68710a342f75d41de50dd8169a01 Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Wed, 20 Mar 2024 14:34:04 +0100 Subject: [PATCH 04/13] More depends fixes --- recipes/illumina-interop/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index b0d7194f5f722..cd4d75edfe6d8 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -21,13 +21,13 @@ requirements: - cmake - {{ compiler('c') }} - {{ compiler('cxx') }} - - python + - python >=3.9 - numpy - swig test: requires: - - python + - python >=3.9 - numpy imports: - interop From f231b06c3c72fdf0e38e0a0ab8b004e68ed3f141 Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Wed, 20 Mar 2024 15:24:36 +0100 Subject: [PATCH 05/13] More depends --- recipes/illumina-interop/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index cd4d75edfe6d8..c7491ee0523b3 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -24,6 +24,7 @@ requirements: - python >=3.9 - numpy - swig + - libgomp # [linux] test: requires: From 6caf8caed620dbf8cdb4d6744d69a4947801a816 Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Wed, 20 Mar 2024 16:54:06 +0100 Subject: [PATCH 06/13] Debug --- recipes/illumina-interop/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index c7491ee0523b3..741c1cd0f8dc2 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -30,9 +30,9 @@ test: requires: - python >=3.9 - numpy - imports: - - interop commands: + - 'ls -Ra lib/python3.1/site-packages' + - 'ls -Ra lib/python3.1/site-packages/interop' - interop_dumptext | grep Version > /dev/null - interop_imaging_table | grep Version > /dev/null - interop_summary | grep Version > /dev/null From fdcbd156db6d6339da19637795ae8248d203a8e7 Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Wed, 20 Mar 2024 17:29:00 +0100 Subject: [PATCH 07/13] debug --- recipes/illumina-interop/meta.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index 741c1cd0f8dc2..b2cfc68ab4288 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -31,8 +31,7 @@ test: - python >=3.9 - numpy commands: - - 'ls -Ra lib/python3.1/site-packages' - - 'ls -Ra lib/python3.1/site-packages/interop' + - 'la -Ra $CONDA_PREFIX/python3.1/site-packages' - interop_dumptext | grep Version > /dev/null - interop_imaging_table | grep Version > /dev/null - interop_summary | grep Version > /dev/null From 31c165bf671f102310a2e8215eb9386d49e5b67f Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Wed, 20 Mar 2024 22:14:59 +0100 Subject: [PATCH 08/13] debug --- recipes/illumina-interop/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index b2cfc68ab4288..03d865e637190 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -31,7 +31,7 @@ test: - python >=3.9 - numpy commands: - - 'la -Ra $CONDA_PREFIX/python3.1/site-packages' + - 'ls -Ra $CONDA_PREFIX/python3.1/site-packages' - interop_dumptext | grep Version > /dev/null - interop_imaging_table | grep Version > /dev/null - interop_summary | grep Version > /dev/null From 7bebd3f874c13a40890889b202377eac9a0eb105 Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Thu, 21 Mar 2024 09:28:32 +0100 Subject: [PATCH 09/13] debug --- recipes/illumina-interop/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index 03d865e637190..9628faf6622df 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -31,7 +31,7 @@ test: - python >=3.9 - numpy commands: - - 'ls -Ra $CONDA_PREFIX/python3.1/site-packages' + - 'ls -Ra $CONDA_PREFIX/lib/python3.1/site-packages' - interop_dumptext | grep Version > /dev/null - interop_imaging_table | grep Version > /dev/null - interop_summary | grep Version > /dev/null From e81a8ec5a8ce11aa2a43dd301c7eb8989b13b3c6 Mon Sep 17 00:00:00 2001 From: Christian Brueffer Date: Thu, 21 Mar 2024 10:49:50 +0100 Subject: [PATCH 10/13] debug --- recipes/illumina-interop/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index 9628faf6622df..26932f19eb707 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -31,7 +31,9 @@ test: - python >=3.9 - numpy commands: - - 'ls -Ra $CONDA_PREFIX/lib/python3.1/site-packages' + - 'ls -Ra $CONDA_PREFIX/lib/' + - 'ls -Ra $CONDA_PREFIX/lib/python3.12' + - 'ls -Ra $CONDA_PREFIX/lib/python3.12/site-packages' - interop_dumptext | grep Version > /dev/null - interop_imaging_table | grep Version > /dev/null - interop_summary | grep Version > /dev/null From 2f1e841c282387c1f7760ba3fa22cf61eaa45d36 Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Mon, 1 Jul 2024 09:44:50 +0300 Subject: [PATCH 11/13] Bump build number Signed-off-by: Martin Tzvetanov Grigorov --- recipes/illumina-interop/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index 19fe55d3c1152..9b6438230a582 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -6,7 +6,7 @@ package: version: '{{version}}' build: - number: 1 + number: 2 skip: true # [osx] run_exports: - {{ pin_subpackage('illumina-interop', max_pin="x.x") }} From 351aad4537c9c4accbe56645bf3df327edf70ea1 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Mon, 1 Jul 2024 10:06:38 +0300 Subject: [PATCH 12/13] List the files of the installed Python version --- recipes/illumina-interop/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index 9b6438230a582..5e4557f276e8c 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -32,8 +32,8 @@ test: - numpy commands: - 'ls -Ra $CONDA_PREFIX/lib/' - - 'ls -Ra $CONDA_PREFIX/lib/python3.12' - - 'ls -Ra $CONDA_PREFIX/lib/python3.12/site-packages' + # - 'ls -Ra $CONDA_PREFIX/lib/python*' + # - 'ls -Ra $CONDA_PREFIX/lib/python*/site-packages' - interop_dumptext | grep Version > /dev/null - interop_imaging_table | grep Version > /dev/null - interop_summary | grep Version > /dev/null From 47237af0b9d6db0d0b944a338ea7f7d5ccaed033 Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Mon, 1 Jul 2024 11:53:07 +0300 Subject: [PATCH 13/13] List the contents of /opt/mambaforge/envs/bioconda/lib/python3*/ Signed-off-by: Martin Tzvetanov Grigorov --- recipes/illumina-interop/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/illumina-interop/meta.yaml b/recipes/illumina-interop/meta.yaml index 5e4557f276e8c..1f042160ff5f6 100644 --- a/recipes/illumina-interop/meta.yaml +++ b/recipes/illumina-interop/meta.yaml @@ -32,8 +32,8 @@ test: - numpy commands: - 'ls -Ra $CONDA_PREFIX/lib/' - # - 'ls -Ra $CONDA_PREFIX/lib/python*' - # - 'ls -Ra $CONDA_PREFIX/lib/python*/site-packages' + - 'ls -Ra /opt/mambaforge/envs/bioconda/lib/python3*' + - 'ls -Ra /opt/mambaforge/envs/bioconda/lib/python3*/site-packages' - interop_dumptext | grep Version > /dev/null - interop_imaging_table | grep Version > /dev/null - interop_summary | grep Version > /dev/null