From 7e2574d9e729d8e3811082e7a841fb9b05a1e16d Mon Sep 17 00:00:00 2001 From: Ofir Shorer <95224651+ofirshorer@users.noreply.github.com> Date: Mon, 29 Sep 2025 15:56:01 +0300 Subject: [PATCH 1/7] Add meta.yaml for scXpand Add the meta.yaml file according to the template provided by the scverse consortium. --- packages/scXpand/meta.yaml | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 packages/scXpand/meta.yaml diff --git a/packages/scXpand/meta.yaml b/packages/scXpand/meta.yaml new file mode 100644 index 00000000..20f8ee3f --- /dev/null +++ b/packages/scXpand/meta.yaml @@ -0,0 +1,25 @@ +name: scXpand +description: | + scXpand is a machine learning framework for pan-cancer detection of T-cell clonal expansion + directly from single-cell RNA sequencing (scRNA-seq), without paired T-cell receptor (TCR) sequencing. +project_home: https://github.com/yizhak-lab-ccg/scXpand +documentation_home: https://scxpand.readthedocs.io/en/latest/ +tutorials_home: https://scxpand.readthedocs.io/en/latest/ +publications: + - 10.1101/2025.09.14.676069 +install: + pypi: scxpand, scxpand-cuda (GPU-supported version) +tags: + - cancer + - scRNA-seq + - scTCR-seq + - T-cell clonal expansion + - machine learning +license: MIT +version: v0.4.1 +authors: + - ronamit + - ofirshorer + - yizhak-lab-ccg +test_command: | + pip install ".[dev]" && pytest From 9d71a11df422ebbe81a74934a0b586901d76fedb Mon Sep 17 00:00:00 2001 From: Ofir Shorer <95224651+ofirshorer@users.noreply.github.com> Date: Mon, 29 Sep 2025 16:21:46 +0300 Subject: [PATCH 2/7] Update meta.yaml --- packages/scXpand/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/scXpand/meta.yaml b/packages/scXpand/meta.yaml index 20f8ee3f..ee6310f1 100644 --- a/packages/scXpand/meta.yaml +++ b/packages/scXpand/meta.yaml @@ -16,7 +16,7 @@ tags: - T-cell clonal expansion - machine learning license: MIT -version: v0.4.1 +version: v0.4.2 authors: - ronamit - ofirshorer From 4e689e61c3e7c941a61a61150abb7af5e10709d3 Mon Sep 17 00:00:00 2001 From: Ofir Shorer <95224651+ofirshorer@users.noreply.github.com> Date: Tue, 30 Sep 2025 09:09:47 +0300 Subject: [PATCH 3/7] Update meta.yaml --- packages/scXpand/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/scXpand/meta.yaml b/packages/scXpand/meta.yaml index ee6310f1..7c2e1144 100644 --- a/packages/scXpand/meta.yaml +++ b/packages/scXpand/meta.yaml @@ -22,4 +22,4 @@ authors: - ofirshorer - yizhak-lab-ccg test_command: | - pip install ".[dev]" && pytest + pip install -e ".[dev]" && pytest --cov=src/scxpand -n auto From 0db9217105274675e988a0e12dd51372019cf4c3 Mon Sep 17 00:00:00 2001 From: Ofir Shorer <95224651+ofirshorer@users.noreply.github.com> Date: Tue, 30 Sep 2025 09:42:01 +0300 Subject: [PATCH 4/7] Update meta.yaml --- packages/scXpand/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/scXpand/meta.yaml b/packages/scXpand/meta.yaml index 7c2e1144..913685f0 100644 --- a/packages/scXpand/meta.yaml +++ b/packages/scXpand/meta.yaml @@ -22,4 +22,4 @@ authors: - ofirshorer - yizhak-lab-ccg test_command: | - pip install -e ".[dev]" && pytest --cov=src/scxpand -n auto + pip install -e ".[dev]" && pytest --cov=src/scxpand --cov-report=xml --cov-fail-under=80 -n auto From 7968980c7c4979278e0cc85a984b9ac9e4a56606 Mon Sep 17 00:00:00 2001 From: Ofir Shorer <95224651+ofirshorer@users.noreply.github.com> Date: Tue, 30 Sep 2025 11:02:08 +0300 Subject: [PATCH 5/7] Update meta.yaml --- packages/scXpand/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/scXpand/meta.yaml b/packages/scXpand/meta.yaml index 913685f0..2f5dcd68 100644 --- a/packages/scXpand/meta.yaml +++ b/packages/scXpand/meta.yaml @@ -16,7 +16,7 @@ tags: - T-cell clonal expansion - machine learning license: MIT -version: v0.4.2 +version: v0.4.3 authors: - ronamit - ofirshorer From 1601638984ce2cec4e66d0cef905a669b4bc3e04 Mon Sep 17 00:00:00 2001 From: Ofir Shorer <95224651+ofirshorer@users.noreply.github.com> Date: Wed, 1 Oct 2025 11:34:30 +0300 Subject: [PATCH 6/7] Update meta.yaml --- packages/scXpand/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/scXpand/meta.yaml b/packages/scXpand/meta.yaml index 2f5dcd68..c57e200b 100644 --- a/packages/scXpand/meta.yaml +++ b/packages/scXpand/meta.yaml @@ -22,4 +22,4 @@ authors: - ofirshorer - yizhak-lab-ccg test_command: | - pip install -e ".[dev]" && pytest --cov=src/scxpand --cov-report=xml --cov-fail-under=80 -n auto + pip install -e ".[dev]" && pytest --cov=src.scxpand tests From 702bc60ee74af3fd97e443b22667fa089948ccf6 Mon Sep 17 00:00:00 2001 From: Ofir Shorer <95224651+ofirshorer@users.noreply.github.com> Date: Wed, 1 Oct 2025 11:41:21 +0300 Subject: [PATCH 7/7] Update meta.yaml --- packages/scXpand/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/packages/scXpand/meta.yaml b/packages/scXpand/meta.yaml index c57e200b..79893e71 100644 --- a/packages/scXpand/meta.yaml +++ b/packages/scXpand/meta.yaml @@ -22,4 +22,4 @@ authors: - ofirshorer - yizhak-lab-ccg test_command: | - pip install -e ".[dev]" && pytest --cov=src.scxpand tests + pip install -e ".[dev]" && pytest --cov=src.scxpand tests