From 8b7f0d830cc726c020ca493da10d013aabd08429 Mon Sep 17 00:00:00 2001 From: Anna Murphy Date: Tue, 27 Aug 2024 16:08:44 -0400 Subject: [PATCH 1/7] add git requirement --- requirements/classes/neur1630/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements/classes/neur1630/requirements.txt b/requirements/classes/neur1630/requirements.txt index a9e46cc..b39ffb1 100644 --- a/requirements/classes/neur1630/requirements.txt +++ b/requirements/classes/neur1630/requirements.txt @@ -1,5 +1,4 @@ # add class-specific packages here: - ipywidgets zarr requests @@ -15,6 +14,7 @@ fastcluster tqdm pynwb dandi +git+https://github.com/alleninstitute/abc_atlas_access # these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE ) dask From acc9c14ceefa373ec8422d48c5291fc288fb03da Mon Sep 17 00:00:00 2001 From: Anna Murphy Date: Tue, 27 Aug 2024 16:14:26 -0400 Subject: [PATCH 2/7] fix typo --- requirements/classes/neur1630/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements/classes/neur1630/requirements.txt b/requirements/classes/neur1630/requirements.txt index b39ffb1..2acd303 100644 --- a/requirements/classes/neur1630/requirements.txt +++ b/requirements/classes/neur1630/requirements.txt @@ -14,7 +14,7 @@ fastcluster tqdm pynwb dandi -git+https://github.com/alleninstitute/abc_atlas_access +git+https://github.com/alleninstitute/abc_atlas_access.git # these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE ) dask From f438889199bd20db1b6f346efa153cc1d1b919c1 Mon Sep 17 00:00:00 2001 From: Anna Murphy Date: Tue, 27 Aug 2024 18:14:31 -0400 Subject: [PATCH 3/7] move dependency to requirements.pip.txt --- requirements/classes/neur1630/requirements.pip.txt | 1 + requirements/classes/neur1630/requirements.txt | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements/classes/neur1630/requirements.pip.txt b/requirements/classes/neur1630/requirements.pip.txt index 3d4fcb0..1ca9b74 100644 --- a/requirements/classes/neur1630/requirements.pip.txt +++ b/requirements/classes/neur1630/requirements.pip.txt @@ -8,3 +8,4 @@ pynapple pybiomart pyranges gseapy +git+https://github.com/alleninstitute/abc_atlas_access.git diff --git a/requirements/classes/neur1630/requirements.txt b/requirements/classes/neur1630/requirements.txt index 2acd303..bb44b13 100644 --- a/requirements/classes/neur1630/requirements.txt +++ b/requirements/classes/neur1630/requirements.txt @@ -14,7 +14,6 @@ fastcluster tqdm pynwb dandi -git+https://github.com/alleninstitute/abc_atlas_access.git # these are the scipy base packages ( YOU PROBABLY DON'T WANT TO REMOVE THESE ) dask From 4028a549957e2be2584fec3816f89f51d7a5c654 Mon Sep 17 00:00:00 2001 From: Anna Murphy Date: Wed, 18 Sep 2024 11:53:50 -0400 Subject: [PATCH 4/7] new pip packages --- requirements/classes/neur1630/requirements.pip.txt | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/requirements/classes/neur1630/requirements.pip.txt b/requirements/classes/neur1630/requirements.pip.txt index 1ca9b74..248dad5 100644 --- a/requirements/classes/neur1630/requirements.pip.txt +++ b/requirements/classes/neur1630/requirements.pip.txt @@ -8,4 +8,9 @@ pynapple pybiomart pyranges gseapy +gdown +rastermap +zenodo-get +cellxgene-census +ONE-api git+https://github.com/alleninstitute/abc_atlas_access.git From e6f9be5ac2a66846361467ef770ef9531ac8eef6 Mon Sep 17 00:00:00 2001 From: Anna Murphy Date: Thu, 26 Sep 2024 14:35:28 -0400 Subject: [PATCH 5/7] remove lost fonts --- Dockerfile | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/Dockerfile b/Dockerfile index 1f5b662..0d56979 100644 --- a/Dockerfile +++ b/Dockerfile @@ -53,16 +53,6 @@ RUN fix-permissions "${CONDA_DIR}" && \ USER root -# Install missing fonts -RUN cd /usr/share/fonts && \ - wget http://mirrors.ctan.org/fonts/tex-gyre/opentype/texgyrepagella-bold.otf && \ - wget http://mirrors.ctan.org/fonts/tex-gyre/opentype/texgyrepagella-bolditalic.otf && \ - wget http://mirrors.ctan.org/fonts/tex-gyre/opentype/texgyrepagella-italic.otf && \ - wget http://mirrors.ctan.org/fonts/tex-gyre/opentype/texgyrepagella-regular.otf && \ - wget https://noto-website-2.storage.googleapis.com/pkgs/NotoSansMono-unhinted.zip && \ - unzip NotoSansMono-unhinted.zip && \ - chmod +r -R /usr/share/fonts - RUN fc-cache -fsv RUN mktexlsr From ec18ade0bdb71f6f3ada6d457c6fe9453d1c5691 Mon Sep 17 00:00:00 2001 From: Anna Murphy Date: Thu, 26 Sep 2024 15:00:27 -0400 Subject: [PATCH 6/7] comment out weir dep --- requirements/classes/neur1630/requirements.pip.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements/classes/neur1630/requirements.pip.txt b/requirements/classes/neur1630/requirements.pip.txt index 248dad5..f3a6f05 100644 --- a/requirements/classes/neur1630/requirements.pip.txt +++ b/requirements/classes/neur1630/requirements.pip.txt @@ -13,4 +13,4 @@ rastermap zenodo-get cellxgene-census ONE-api -git+https://github.com/alleninstitute/abc_atlas_access.git +#git+https://github.com/alleninstitute/abc_atlas_access.git From fa43c7c9279de42b43c551fb894614c325256aa1 Mon Sep 17 00:00:00 2001 From: Anna Murphy Date: Fri, 27 Sep 2024 14:29:31 -0400 Subject: [PATCH 7/7] lock pyyaml version --- requirements/classes/neur1630/requirements.pip.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/requirements/classes/neur1630/requirements.pip.txt b/requirements/classes/neur1630/requirements.pip.txt index f3a6f05..e920aea 100644 --- a/requirements/classes/neur1630/requirements.pip.txt +++ b/requirements/classes/neur1630/requirements.pip.txt @@ -13,4 +13,5 @@ rastermap zenodo-get cellxgene-census ONE-api -#git+https://github.com/alleninstitute/abc_atlas_access.git +git+https://github.com/alleninstitute/abc_atlas_access.git +PyYAML>=6.0.0