From 40a2e43fa9850d27ba784323e813b2b695983404 Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 17 Jul 2024 23:45:30 -0700 Subject: [PATCH 1/6] update conda env files - only use conda-forge channel (removed defaults) - install MDAnalysis via conda instead of pip --- devtools/conda-envs/environment.yaml | 6 +----- devtools/conda-envs/test_env.yaml | 6 +----- devtools/conda-envs/test_min.yaml | 6 +----- 3 files changed, 3 insertions(+), 15 deletions(-) diff --git a/devtools/conda-envs/environment.yaml b/devtools/conda-envs/environment.yaml index 11e976d..8487f9d 100644 --- a/devtools/conda-envs/environment.yaml +++ b/devtools/conda-envs/environment.yaml @@ -1,12 +1,8 @@ name: membrane-curvature channels: - conda-forge - - defaults dependencies: - python - pip - numpy - - # Pip-only installs - - pip: - - MDAnalysis>=2.0.0b0 + - MDAnalysis>=2.0.0 diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index fd4572e..1ca92ba 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -1,7 +1,6 @@ name: test channels: - conda-forge - - defaults dependencies: - python - pip @@ -11,7 +10,4 @@ dependencies: - pytest - pytest-cov - codecov - - # Pip-only installs - - pip: - - MDAnalysis>=2.0.0 + - MDAnalysis>=2.0.0 diff --git a/devtools/conda-envs/test_min.yaml b/devtools/conda-envs/test_min.yaml index a177c53..94bb12c 100644 --- a/devtools/conda-envs/test_min.yaml +++ b/devtools/conda-envs/test_min.yaml @@ -1,7 +1,6 @@ name: test channels: - conda-forge - - defaults dependencies: - python - pip @@ -11,7 +10,4 @@ dependencies: - pytest - pytest-cov - codecov - - # Pip-only installs - - pip: - - MDAnalysis==2.0.0 + - MDAnalysis==2.0.0 From 6ffcc55b11d7e077d07138c0d227a14fcf2f041e Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Thu, 18 Jul 2024 14:45:55 +0100 Subject: [PATCH 2/6] Update environment.yaml --- devtools/conda-envs/environment.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/devtools/conda-envs/environment.yaml b/devtools/conda-envs/environment.yaml index 8487f9d..635875c 100644 --- a/devtools/conda-envs/environment.yaml +++ b/devtools/conda-envs/environment.yaml @@ -4,5 +4,4 @@ channels: dependencies: - python - pip - - numpy - MDAnalysis>=2.0.0 From 9e6d4771b49f5f006d31b4ba243786c71961ba5f Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Thu, 18 Jul 2024 14:46:19 +0100 Subject: [PATCH 3/6] Update test_env.yaml --- devtools/conda-envs/test_env.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index 1ca92ba..0e6dd6c 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -4,10 +4,9 @@ channels: dependencies: - python - pip - - numpy - sphinx + - MDAnalysis>=2.0.0 # Testing - pytest - pytest-cov - codecov - - MDAnalysis>=2.0.0 From bf1011fbc1ababbd8de51545341fdbb20ad1eacb Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Thu, 18 Jul 2024 14:46:36 +0100 Subject: [PATCH 4/6] Update test_min.yaml --- devtools/conda-envs/test_min.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-envs/test_min.yaml b/devtools/conda-envs/test_min.yaml index 94bb12c..9ca84b4 100644 --- a/devtools/conda-envs/test_min.yaml +++ b/devtools/conda-envs/test_min.yaml @@ -5,9 +5,9 @@ dependencies: - python - pip - numpy==1.20.0 + - MDAnalysis==2.0.0 - sphinx # Testing - pytest - pytest-cov - codecov - - MDAnalysis==2.0.0 From fcb8b5567d3eb3f8dc581dcbf9816c5f7ff67655 Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Thu, 18 Jul 2024 14:55:29 +0100 Subject: [PATCH 5/6] Update test_min.yaml --- devtools/conda-envs/test_min.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-envs/test_min.yaml b/devtools/conda-envs/test_min.yaml index 9ca84b4..5e2f710 100644 --- a/devtools/conda-envs/test_min.yaml +++ b/devtools/conda-envs/test_min.yaml @@ -4,7 +4,7 @@ channels: dependencies: - python - pip - - numpy==1.20.0 + - numpy==1.21.0 - MDAnalysis==2.0.0 - sphinx # Testing From d579f445504d678863b97d807d7ec2f9f4966d0a Mon Sep 17 00:00:00 2001 From: Irfan Alibay Date: Thu, 18 Jul 2024 15:00:21 +0100 Subject: [PATCH 6/6] Update pyproject.toml --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 8c8545d..530be0f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,9 +21,9 @@ keywords = [ "trajectory-analysis", ] dependencies = [ - 'numpy>=1.20.0', + 'numpy>=1.21.0', 'mdanalysis>=2.0.0' - ] +] classifiers = [ 'Development Status :: 5 - Production/Stable',