From e07eed7de6e0290f8fd3021ea592ae3e8eb157b7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sat, 10 Aug 2024 13:43:20 +0200 Subject: [PATCH 01/12] Create meta.yaml --- packages/scPRINT/meta.yaml | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 packages/scPRINT/meta.yaml diff --git a/packages/scPRINT/meta.yaml b/packages/scPRINT/meta.yaml new file mode 100644 index 00000000..7ec87237 --- /dev/null +++ b/packages/scPRINT/meta.yaml @@ -0,0 +1,26 @@ +name: scPRINT +description: | + A single cell foundation model for Gene network inference and more... +project_home: https://github.com/cantinilab/scPRINT +documentation_home: https://jkobject.com/scPRINT +publications: + - 10.1101/2024.07.29.605556 +install: + pypi: scprint +tags: + - foundation model + - single cell + - RNAseq + - gene network inference + - denoising + - zero imputation + - label prediction + - zero shot + - embedding + - pytorch + - lightning +license: MIT +version: v1.0.12 +authors: + - jkobject (jeremie kalfon) +test_command: pip install . && make test From 16dcf19fd5fe1094f79778afbbfb3d76f80e5d56 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sat, 10 Aug 2024 13:43:42 +0200 Subject: [PATCH 02/12] Create meta.yaml --- packages/scDataLoader/meta.yaml | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 packages/scDataLoader/meta.yaml diff --git a/packages/scDataLoader/meta.yaml b/packages/scDataLoader/meta.yaml new file mode 100644 index 00000000..02d5a92a --- /dev/null +++ b/packages/scDataLoader/meta.yaml @@ -0,0 +1,24 @@ +name: scDataLoader +description: | + A dataloader for large single cell databases like cellxgene. + Does weighted random sampling, downloading and preprocessing. + works with anndata, zarr, and h5ad files. +project_home: https://github.com/jkobject/scDataLoader +documentation_home: https://jkobject.com/scDataLoader +publications: + - 10.1101/2024.07.29.605556 +install: + pypi: scdataloader +tags: + - dataloader + - single cell + - RNAseq + - pytorch + - lightning + - cellxgene + - preprocessing +license: MIT +version: v1.0.1 +authors: + - jkobject (jeremie kalfon) +test_command: pip install . && make test From 2104287d01475ad2324ce48953d398237622230c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sat, 10 Aug 2024 13:46:47 +0200 Subject: [PATCH 03/12] Create meta.yaml --- packages/benGRN/meta.yaml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 packages/benGRN/meta.yaml diff --git a/packages/benGRN/meta.yaml b/packages/benGRN/meta.yaml new file mode 100644 index 00000000..2c1948fb --- /dev/null +++ b/packages/benGRN/meta.yaml @@ -0,0 +1,20 @@ +name: benGRN +description: | + Benchmarking tool for gene network inference from single cell RNAseq methods. + It uses the grnndata/anndata modality and only contains biological ground truth networks +project_home: https://github.com/jkobject/benGRN +documentation_home: https://jkobject.com/benGRN +publications: + - 10.1101/2024.07.29.605556 +install: + pypi: bengrn +tags: + - single cell + - RNAseq + - gene network inference + - benchmark +license: MIT +version: v1.0.1 +authors: + - jkobject (jeremie kalfon) +test_command: pip install . && make test From ee979425b858af3cec514c6775a448ddf91c0894 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sat, 10 Aug 2024 13:47:27 +0200 Subject: [PATCH 04/12] Create meta.yaml --- packages/GRnnData/meta.yaml | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 packages/GRnnData/meta.yaml diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml new file mode 100644 index 00000000..0a4ebbfe --- /dev/null +++ b/packages/GRnnData/meta.yaml @@ -0,0 +1,21 @@ +name: GRnnData +description: | + An onverload of anndata to more easily work with gene networks. + Allows easy conversion between anndata and grnndata and provide loads of usefull utilities functions. +project_home: https://github.com/cantinilab/GRnnData +documentation_home: https://jkobject.com/GRnnData +publications: + - 10.1101/2024.07.29.605556 +install: + pypi: grnndata +tags: + - single cell + - RNAseq + - gene networks + - format + - utilities +license: MIT +version: v1.0.0 +authors: + - jkobject (jeremie kalfon) +test_command: pip install . && make test From a86f3e2dd654479c793dd802bce1a1cd47a2c76f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Wed, 13 Nov 2024 14:55:14 +0100 Subject: [PATCH 05/12] Update meta.yaml --- packages/benGRN/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/benGRN/meta.yaml b/packages/benGRN/meta.yaml index 2c1948fb..43d716b3 100644 --- a/packages/benGRN/meta.yaml +++ b/packages/benGRN/meta.yaml @@ -3,7 +3,7 @@ description: | Benchmarking tool for gene network inference from single cell RNAseq methods. It uses the grnndata/anndata modality and only contains biological ground truth networks project_home: https://github.com/jkobject/benGRN -documentation_home: https://jkobject.com/benGRN +documentation_home: https://www.jkobject.com/benGRN publications: - 10.1101/2024.07.29.605556 install: @@ -14,7 +14,7 @@ tags: - gene network inference - benchmark license: MIT -version: v1.0.1 +version: v1.2.1 authors: - jkobject (jeremie kalfon) test_command: pip install . && make test From aa7a3faac368c3b1644ef27160b0846ca99f27ee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Wed, 13 Nov 2024 15:00:14 +0100 Subject: [PATCH 06/12] Update meta.yaml --- packages/GRnnData/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml index 0a4ebbfe..d3983e8a 100644 --- a/packages/GRnnData/meta.yaml +++ b/packages/GRnnData/meta.yaml @@ -3,7 +3,7 @@ description: | An onverload of anndata to more easily work with gene networks. Allows easy conversion between anndata and grnndata and provide loads of usefull utilities functions. project_home: https://github.com/cantinilab/GRnnData -documentation_home: https://jkobject.com/GRnnData +documentation_home: https://cantinilab.github.io/GRnnData/ publications: - 10.1101/2024.07.29.605556 install: @@ -15,7 +15,7 @@ tags: - format - utilities license: MIT -version: v1.0.0 +version: v1.1.4 authors: - jkobject (jeremie kalfon) test_command: pip install . && make test From a68d8e2963c5ea9884a85a80c32af463cdff4a73 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Wed, 13 Nov 2024 15:08:56 +0100 Subject: [PATCH 07/12] Update meta.yaml --- packages/scDataLoader/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/scDataLoader/meta.yaml b/packages/scDataLoader/meta.yaml index 02d5a92a..115553f7 100644 --- a/packages/scDataLoader/meta.yaml +++ b/packages/scDataLoader/meta.yaml @@ -4,7 +4,7 @@ description: | Does weighted random sampling, downloading and preprocessing. works with anndata, zarr, and h5ad files. project_home: https://github.com/jkobject/scDataLoader -documentation_home: https://jkobject.com/scDataLoader +documentation_home: https://www.jkobject.com/scDataLoader/ publications: - 10.1101/2024.07.29.605556 install: @@ -18,7 +18,7 @@ tags: - cellxgene - preprocessing license: MIT -version: v1.0.1 +version: v1.2.2 authors: - jkobject (jeremie kalfon) test_command: pip install . && make test From 81a4a4fd98bd4ca530662561d842f2e67ef86764 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Wed, 13 Nov 2024 15:11:22 +0100 Subject: [PATCH 08/12] Update meta.yaml --- packages/scPRINT/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/packages/scPRINT/meta.yaml b/packages/scPRINT/meta.yaml index 7ec87237..5fbf626a 100644 --- a/packages/scPRINT/meta.yaml +++ b/packages/scPRINT/meta.yaml @@ -2,7 +2,7 @@ name: scPRINT description: | A single cell foundation model for Gene network inference and more... project_home: https://github.com/cantinilab/scPRINT -documentation_home: https://jkobject.com/scPRINT +documentation_home: https://cantinilab.github.io/scPRINT/ publications: - 10.1101/2024.07.29.605556 install: @@ -20,7 +20,7 @@ tags: - pytorch - lightning license: MIT -version: v1.0.12 +version: v1.6.2 authors: - jkobject (jeremie kalfon) test_command: pip install . && make test From 04853c064533a1b0a7c280374a79dc81e187f0f9 Mon Sep 17 00:00:00 2001 From: jkobject Date: Sun, 28 Dec 2025 17:00:16 +0100 Subject: [PATCH 09/12] adding scprint-2 and scprint --- packages/scPRINT-2/meta.yaml | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 packages/scPRINT-2/meta.yaml diff --git a/packages/scPRINT-2/meta.yaml b/packages/scPRINT-2/meta.yaml new file mode 100644 index 00000000..6fa67b5e --- /dev/null +++ b/packages/scPRINT-2/meta.yaml @@ -0,0 +1,29 @@ +name: scPRINT-2 +description: | + A next generation single cell foundation model +project_home: https://github.com/cantinilab/scPRINT-2 +documentation_home: https://cantinilab.github.io/scPRINT-2/ +publications: + - 10.64898/2025.12.11.693702v2 +install: + pypi: scprint2 +tags: + - foundation model + - single cell + - RNAseq + - gene network inference + - denoising + - zero imputation + - label prediction + - zero shot + - embedding + - pytorch + - lightning + - species integration + - expression imputation + - counterfactual predictions +license: GPL-3.0-or-later +version: v1.0.0 +authors: + - jkobject (jeremie kalfon) +test_command: pip install . && make test From 9e42b5baecef17c14615a8d7be665b2c597e630f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sun, 28 Dec 2025 17:45:45 +0100 Subject: [PATCH 10/12] Add contact information to authors in meta.yaml Updated authors section to include contact information. --- packages/scPRINT-2/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/scPRINT-2/meta.yaml b/packages/scPRINT-2/meta.yaml index 6fa67b5e..52d52b88 100644 --- a/packages/scPRINT-2/meta.yaml +++ b/packages/scPRINT-2/meta.yaml @@ -24,6 +24,6 @@ tags: - counterfactual predictions license: GPL-3.0-or-later version: v1.0.0 -authors: +contact: - jkobject (jeremie kalfon) test_command: pip install . && make test From 65666a98dcd8bc8cd3d1a9bb61d04c3ce6a18ab2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sun, 28 Dec 2025 17:47:10 +0100 Subject: [PATCH 11/12] Apply suggestions from code review Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- packages/GRnnData/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml index dda919bc..85b63c06 100644 --- a/packages/GRnnData/meta.yaml +++ b/packages/GRnnData/meta.yaml @@ -1,7 +1,7 @@ name: GRnnData description: | An onverload of anndata to more easily work with gene networks. - Allows easy conversion between anndata and grnndata and provide loads of usefull utilities functions. + Allows easy conversion between anndata and grnndata and provide loads of useful utilities functions. project_home: https://github.com/cantinilab/GRnnData documentation_home: https://cantinilab.github.io/GRnnData/ publications: From 6e78a97ef5672af51c07f99778196297bd614b50 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=A9r=C3=A9mie=20Kalfon?= Date: Sun, 28 Dec 2025 17:47:18 +0100 Subject: [PATCH 12/12] Apply suggestion from @Copilot Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --- packages/GRnnData/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml index 85b63c06..6e07988d 100644 --- a/packages/GRnnData/meta.yaml +++ b/packages/GRnnData/meta.yaml @@ -1,6 +1,6 @@ name: GRnnData description: | - An onverload of anndata to more easily work with gene networks. + An overload of anndata to more easily work with gene networks. Allows easy conversion between anndata and grnndata and provide loads of useful utilities functions. project_home: https://github.com/cantinilab/GRnnData documentation_home: https://cantinilab.github.io/GRnnData/