From 0b29fa02f85b7af2688c7b90c492e6d37cc0da2a Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Thu, 13 Aug 2026 10:55:48 +0200
Subject: [PATCH 01/11] fix kbet_pg and kbet_pg_label failing to build

pandas<2.0 and numpy<2.0 no longer resolve to anything that builds on
the base image, and pegasuspy doesn't ask for them -- it wants
pandas>=1.2.0 and declares zarr<3 itself, so all three bounds can go.

That gets the image building again, but pegasus imports pkg_resources,
which setuptools dropped in 81, so pin setuptools under that.

* drop zarr, pandas and numpy bounds from both components
* add setuptools<81
---
 src/metrics/kbet_pg/config.vsh.yaml       | 4 +---
 src/metrics/kbet_pg_label/config.vsh.yaml | 4 +---
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/src/metrics/kbet_pg/config.vsh.yaml b/src/metrics/kbet_pg/config.vsh.yaml
index 6f35a94c5..50feeddda 100644
--- a/src/metrics/kbet_pg/config.vsh.yaml
+++ b/src/metrics/kbet_pg/config.vsh.yaml
@@ -39,9 +39,7 @@ engines:
       - type: python
         pypi:
           - pegasuspy
-          - zarr<3.0
-          - pandas<2.0
-          - numpy<2.0
+          - setuptools<81
 runners:
   - type: executable
   - type: nextflow
diff --git a/src/metrics/kbet_pg_label/config.vsh.yaml b/src/metrics/kbet_pg_label/config.vsh.yaml
index f5fbf1f62..2434133ff 100644
--- a/src/metrics/kbet_pg_label/config.vsh.yaml
+++ b/src/metrics/kbet_pg_label/config.vsh.yaml
@@ -39,9 +39,7 @@ engines:
       - type: python
         pypi:
           - pegasuspy
-          - zarr<3.0
-          - pandas<2.0
-          - numpy<2.0
+          - setuptools<81
 runners:
   - type: executable
   - type: nextflow

From 61e00457eaeac305fc480bcbf73fa7af4aa59c5a Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Thu, 13 Aug 2026 10:55:48 +0200
Subject: [PATCH 02/11] fix harmonypy writing a transposed embedding

harmonypy 2.0 returns Z_corr as cells x pcs, where it used to be the
other way around, so the transpose we were doing now hands anndata a
(50, 600) array for a 600 cell dataset and it refuses it.

* drop the transpose
* require harmonypy>=2
---
 src/methods/harmonypy/config.vsh.yaml | 2 +-
 src/methods/harmonypy/script.py       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/methods/harmonypy/config.vsh.yaml b/src/methods/harmonypy/config.vsh.yaml
index 14b02e73f..8b1a66265 100644
--- a/src/methods/harmonypy/config.vsh.yaml
+++ b/src/methods/harmonypy/config.vsh.yaml
@@ -26,7 +26,7 @@ engines:
     setup:
       - type: python
         pypi:
-          - harmonypy
+          - harmonypy>=2
 runners:
   - type: executable
   - type: nextflow
diff --git a/src/methods/harmonypy/script.py b/src/methods/harmonypy/script.py
index ec8519538..b5a98cc85 100644
--- a/src/methods/harmonypy/script.py
+++ b/src/methods/harmonypy/script.py
@@ -38,7 +38,7 @@
     obs=adata.obs[[]],
     var=adata.var[[]],
     obsm={
-        "X_emb": out.Z_corr.transpose()
+        "X_emb": out.Z_corr
     },
     shape=adata.shape,
     uns={

From 994d1c58bc62202fbbb7af3b54f76986b067bfd5 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Thu, 13 Aug 2026 10:58:57 +0200
Subject: [PATCH 03/11] fix stacas erroring on a defunct GetAssayData argument

STACAS 2.3.0 calls GetAssayData(slot = ), which SeuratObject made
defunct in 5.0.0, so Run.STACAS dies while preparing the PCA
embeddings. Upstream fixed this in carmonalab/STACAS@9a85ec4c but
hasn't cut a release since, so track master until they do.
---
 src/methods/stacas/config.vsh.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/methods/stacas/config.vsh.yaml b/src/methods/stacas/config.vsh.yaml
index 7e0c9735a..e7c8079dd 100644
--- a/src/methods/stacas/config.vsh.yaml
+++ b/src/methods/stacas/config.vsh.yaml
@@ -29,7 +29,7 @@ engines:
     image: openproblems/base_r:1
     setup:
       - type: r
-        github: carmonalab/STACAS@2.3.0
+        github: carmonalab/STACAS
 runners:
   - type: executable
   - type: nextflow

From 9cd163135cb992c68a949f6e590565a85f4761e4 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Thu, 13 Aug 2026 11:22:36 +0200
Subject: [PATCH 04/11] fix scalex failing to build

numpy<1.24 and torch<2.1 contradict what scalex 1.0.4 asks for
(numpy>=1.26.4, torch>=2.2.2), so pip fell back to building an ancient
numpy from source and gave up on setuptools.build_meta.

Dropping both gets it building, but scalex still calls np.Inf, which
numpy 2 removed and upstream hasn't fixed, so it needs numpy<2 rather
than no bound at all.
---
 src/methods/scalex/config.vsh.yaml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/methods/scalex/config.vsh.yaml b/src/methods/scalex/config.vsh.yaml
index 7761592f1..59c1aed46 100644
--- a/src/methods/scalex/config.vsh.yaml
+++ b/src/methods/scalex/config.vsh.yaml
@@ -28,8 +28,7 @@ engines:
       - type: python
         pypi:
           - scalex
-          - numpy<1.24
-          - torch<2.1
+          - numpy<2
 runners:
   - type: executable
   - type: nextflow

From a0de7399c28da8864f4f993debaea5e76fb4efc5 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Thu, 13 Aug 2026 11:25:47 +0200
Subject: [PATCH 05/11] update changelog

---
 CHANGELOG.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9a515e17f..6205814fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,6 +37,13 @@
 * Update scPRINT to use latest stable version (PR #70)
 * Fix kbet dependencies to numpy<2 and scipy<=1.13 (PR #78).
 * Fix `render_readme` crashing on `comp_process_integration.yaml`'s absolute `__merge__` paths.
+* Fix `metrics/kbet_pg` and `metrics/kbet_pg_label` failing to build: drop the zarr, pandas and numpy bounds pegasuspy
+    doesn't ask for, and pin `setuptools<81` so `pkg_resources` is still there.
+* Fix `methods/harmonypy` writing a transposed embedding: harmonypy 2.0 returns `Z_corr` as cells x pcs.
+* Fix `methods/stacas` erroring on `GetAssayData(slot = )`, defunct since SeuratObject 5.0.0. Tracks STACAS master
+    until upstream cuts a release containing the fix.
+* Fix `methods/scalex` failing to build: its numpy and torch bounds contradicted what scalex asks for. Keeps
+    `numpy<2`, since scalex still calls `np.Inf`.
 
 * Split Scanorama into two methods/scores
     - Split Scanorama into embedding (integrate) and count-correction (correct) modes, instead of running both together. 

From c971679b2e0a1954e149ba5007fbc904fd779095 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Thu, 13 Aug 2026 11:29:30 +0200
Subject: [PATCH 06/11] fix pyliger failing to build

pyliger pulls in louvain, which has no wheel for python 3.12 and so
builds igraph's C core from source. That needs cmake, which isn't in
the base image, so the wheel build gave up.
---
 CHANGELOG.md                        | 1 +
 src/methods/pyliger/config.vsh.yaml | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6205814fa..c8cd4ea62 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -44,6 +44,7 @@
     until upstream cuts a release containing the fix.
 * Fix `methods/scalex` failing to build: its numpy and torch bounds contradicted what scalex asks for. Keeps
     `numpy<2`, since scalex still calls `np.Inf`.
+* Fix `methods/pyliger` failing to build: louvain has no python 3.12 wheel and needs cmake to build igraph from source.
 
 * Split Scanorama into two methods/scores
     - Split Scanorama into embedding (integrate) and count-correction (correct) modes, instead of running both together. 
diff --git a/src/methods/pyliger/config.vsh.yaml b/src/methods/pyliger/config.vsh.yaml
index f891770f7..bfbf5933f 100644
--- a/src/methods/pyliger/config.vsh.yaml
+++ b/src/methods/pyliger/config.vsh.yaml
@@ -28,6 +28,8 @@ engines:
   - type: docker
     image: openproblems/base_python:1
     setup:
+      - type: apt
+        packages: [cmake]
       - type: python
         pypi:
           - pyliger

From c6ee38b134115fbd64cc6ccfe1b09c9aff894731 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Thu, 13 Aug 2026 11:40:39 +0200
Subject: [PATCH 07/11] bump stale base images to :1

cellplm, condo, drvi and bras were still on :1.0.0, which carries an
openproblems too old for the component tests in common now that those
import check_config and run_and_check_output from openproblems.project
rather than inlining them.

Every other component was already on :1.
---
 CHANGELOG.md                        | 2 ++
 src/methods/cellplm/config.vsh.yaml | 2 +-
 src/methods/condo/config.vsh.yaml   | 2 +-
 src/methods/drvi/config.vsh.yaml    | 2 +-
 src/metrics/bras/config.vsh.yaml    | 2 +-
 5 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c8cd4ea62..a3e78e280 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -45,6 +45,8 @@
 * Fix `methods/scalex` failing to build: its numpy and torch bounds contradicted what scalex asks for. Keeps
     `numpy<2`, since scalex still calls `np.Inf`.
 * Fix `methods/pyliger` failing to build: louvain has no python 3.12 wheel and needs cmake to build igraph from source.
+* Bump `methods/cellplm`, `methods/condo`, `methods/drvi` and `metrics/bras` from base image `:1.0.0` to `:1`, so their
+    `openproblems` is new enough for the component tests in `common`.
 
 * Split Scanorama into two methods/scores
     - Split Scanorama into embedding (integrate) and count-correction (correct) modes, instead of running both together. 
diff --git a/src/methods/cellplm/config.vsh.yaml b/src/methods/cellplm/config.vsh.yaml
index df8b9e713..6b929b50e 100755
--- a/src/methods/cellplm/config.vsh.yaml
+++ b/src/methods/cellplm/config.vsh.yaml
@@ -38,7 +38,7 @@ resources:
 
 engines:
   - type: docker
-    image: openproblems/base_pytorch_nvidia:1.0.0
+    image: openproblems/base_pytorch_nvidia:1
     setup:
       - type: python
         pypi:
diff --git a/src/methods/condo/config.vsh.yaml b/src/methods/condo/config.vsh.yaml
index 16594d1d1..bb354a1b1 100644
--- a/src/methods/condo/config.vsh.yaml
+++ b/src/methods/condo/config.vsh.yaml
@@ -100,7 +100,7 @@ resources:
   - path: /src/utils/read_anndata_partial.py
 engines:
   - type: docker
-    image: openproblems/base_pytorch_nvidia:1.0.0
+    image: openproblems/base_pytorch_nvidia:1
     setup:
       - type: python
         pypi:
diff --git a/src/methods/drvi/config.vsh.yaml b/src/methods/drvi/config.vsh.yaml
index aed323c22..06b03b1c1 100644
--- a/src/methods/drvi/config.vsh.yaml
+++ b/src/methods/drvi/config.vsh.yaml
@@ -30,7 +30,7 @@ resources:
   - path: /src/utils/read_anndata_partial.py
 engines:
   - type: docker
-    image: openproblems/base_pytorch_nvidia:1.0.0 
+    image: openproblems/base_pytorch_nvidia:1
     setup:
       - type: python
         pypi:
diff --git a/src/metrics/bras/config.vsh.yaml b/src/metrics/bras/config.vsh.yaml
index d40139738..6b46988cf 100644
--- a/src/metrics/bras/config.vsh.yaml
+++ b/src/metrics/bras/config.vsh.yaml
@@ -27,7 +27,7 @@ resources:
 
 engines:
   - type: docker
-    image: openproblems/base_python:1.0.0
+    image: openproblems/base_python:1
     setup:
       - type: python
         pypi:

From c0ab48e809bb9e11c77a2e50e587674c5d492a45 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Thu, 13 Aug 2026 12:03:47 +0200
Subject: [PATCH 08/11] fix geneformer failing to build

pip clones git+ urls with --filter=blob:none, and huggingface's git
server no longer serves that properly:

    fatal: expected 'packfile'
    fatal: could not fetch ... from promisor remote

So clone it ourselves without the filter and install from the checkout.
It's a 3.6 MB clone -- the model files come from hf_hub_download at
runtime, not from git.

That gets it building, but geneformer then imports SpecialTokensMixin,
which transformers dropped in 5, and the base image ships 5.15.
---
 src/methods/geneformer/config.vsh.yaml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/methods/geneformer/config.vsh.yaml b/src/methods/geneformer/config.vsh.yaml
index 35c9e69ae..c836cd716 100644
--- a/src/methods/geneformer/config.vsh.yaml
+++ b/src/methods/geneformer/config.vsh.yaml
@@ -54,7 +54,10 @@ engines:
         pip:
           - pyarrow<15.0.0a0,>=14.0.1
           - huggingface_hub
-          - git+https://huggingface.co/ctheodoris/Geneformer.git
+      - type: docker
+        run: |
+          git clone --depth 1 https://huggingface.co/ctheodoris/Geneformer.git /opt/Geneformer && \
+            pip install --no-cache-dir /opt/Geneformer "transformers<5"
 
 runners:
   - type: executable

From 1dbcf0c618641db631783a6833421e49e2b01e4e Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Thu, 13 Aug 2026 12:16:56 +0200
Subject: [PATCH 09/11] fix cellplm failing to build

cellplm pulls in louvain, which builds igraph's C core and so needs
cmake. The pytorch base image ships a /usr/local/bin/cmake that is a
python shim:

    #!/usr/bin/python3
    from cmake import cmake

/usr/bin/python3 can't see the pip-installed cmake module, so the shim
always dies with ModuleNotFoundError, and it shadows anything we apt
install. Install cmake from apt and drop the shim.
---
 src/methods/cellplm/config.vsh.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/methods/cellplm/config.vsh.yaml b/src/methods/cellplm/config.vsh.yaml
index 6b929b50e..f903b9fba 100755
--- a/src/methods/cellplm/config.vsh.yaml
+++ b/src/methods/cellplm/config.vsh.yaml
@@ -40,6 +40,10 @@ engines:
   - type: docker
     image: openproblems/base_pytorch_nvidia:1
     setup:
+      - type: apt
+        packages: [cmake]
+      - type: docker
+        run: rm -f /usr/local/bin/cmake
       - type: python
         pypi:
           - cellplm

From bc561b21b522a6f79e04c900b0406b3226ddd803 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Thu, 13 Aug 2026 12:16:56 +0200
Subject: [PATCH 10/11] bump drvi-py to 0.2.7

0.1.7 pins scvi-tools 1.0.4, which drags numpy back to 1.26 while the
base image's zarr 3.3 wants numpy>=2, so the test died in zarr on
numpy.dtypes.StringDType. Pinning zarr<3 instead only moved the problem
to torch 2.3.1 missing torch.library.register_fake.

Note this changes the drvi results, it's a two minor version jump.
---
 src/methods/drvi/config.vsh.yaml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/methods/drvi/config.vsh.yaml b/src/methods/drvi/config.vsh.yaml
index 06b03b1c1..2c2a26968 100644
--- a/src/methods/drvi/config.vsh.yaml
+++ b/src/methods/drvi/config.vsh.yaml
@@ -34,9 +34,7 @@ engines:
     setup:
       - type: python
         pypi:
-        - drvi-py==0.1.7
-        - torch==2.3.0
-        - torchvision==0.18.0
+        - drvi-py==0.2.7
 runners:
   - type: executable
   - type: nextflow

From d870c774fde751ff757c61452645141bbc34f4ce Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Thu, 13 Aug 2026 12:57:11 +0200
Subject: [PATCH 11/11] fix scgpt_zeroshot and scgpt_finetuned failing to build

flash-attn never built, and it turns out we don't need it: both scripts
pass use_fast_transformer=False, so it was only ever slowing the image
down. Dropping it uncovered three more pins with no python 3.12 wheels,
each of which sent pip off to build from source:

* numpy<1.24 -> numpy<2, resolves to 1.26.4
* torchtext==0.17.0 -> 0.17.2, the release that goes with torch 2.2
* transformers==4.33.2 -> 4.36.2, since 4.33 wants tokenizers<0.14 and
  building those needs a rust toolchain

Left torch, scvi-tools, datasets and cell-gears where they were, they
don't block the build.
---
 CHANGELOG.md                                |  7 +++++++
 src/methods/scgpt_finetuned/config.vsh.yaml | 11 +----------
 src/methods/scgpt_finetuned/script.py       |  2 +-
 src/methods/scgpt_zeroshot/config.vsh.yaml  | 11 +----------
 4 files changed, 10 insertions(+), 21 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index a3e78e280..0b88e8d69 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -47,6 +47,13 @@
 * Fix `methods/pyliger` failing to build: louvain has no python 3.12 wheel and needs cmake to build igraph from source.
 * Bump `methods/cellplm`, `methods/condo`, `methods/drvi` and `metrics/bras` from base image `:1.0.0` to `:1`, so their
     `openproblems` is new enough for the component tests in `common`.
+* Fix `methods/geneformer` failing to build: pip's `--filter=blob:none` clone of the huggingface repo no longer works,
+    so clone it ourselves. Also needs `transformers<5`, which still has `SpecialTokensMixin`.
+* Fix `methods/cellplm` failing to build: drop the pytorch base image's broken `/usr/local/bin/cmake` shim, which
+    shadowed the apt cmake that louvain needs.
+* Fix `methods/scgpt_zeroshot` and `methods/scgpt_finetuned` failing to build: stop installing `flash-attn`. Both
+    scripts pass `use_fast_transformer=False`, so it was never used. Behind it sat three more pins with no python 3.12
+    wheels, now `numpy<2`, `torchtext==0.17.2` and `transformers==4.36.2`.
 
 * Split Scanorama into two methods/scores
     - Split Scanorama into embedding (integrate) and count-correction (correct) modes, instead of running both together. 
diff --git a/src/methods/scgpt_finetuned/config.vsh.yaml b/src/methods/scgpt_finetuned/config.vsh.yaml
index 2b949cbbe..631a0dfae 100644
--- a/src/methods/scgpt_finetuned/config.vsh.yaml
+++ b/src/methods/scgpt_finetuned/config.vsh.yaml
@@ -49,21 +49,12 @@ resources:
 engines:
   - type: docker
     image: openproblems/base_pytorch_nvidia:1
-    # TODO: Try to find working installation of flash attention (flash-attn<1.0.5)
     setup:
-      #- type: python
-      #  pypi:
-      #    - gdown
-      #    - scgpt # Install from PyPI to get dependencies
-      #- type: docker
-      #  # Force re-installing from GitHub to get bug fixes
-      #  run: pip install --upgrade --no-deps --force-reinstall git+https://github.com/bowang-lab/scGPT.git
       - type: docker
         run: |
           git clone https://github.com/bowang-lab/scGPT && \
           pip install torch==2.2.0 torchvision==0.17.0 torchaudio==2.2.0 --index-url https://download.pytorch.org/whl/cu121 && \
-          pip install "flash-attn<1.0.5" --no-build-isolation && \
-          pip install ipykernel pandas scanpy numba "numpy<1.24" torchtext==0.17.0 scib "scvi-tools<1.0" datasets==2.14.5 transformers==4.33.2 wandb "cell-gears<0.0.3" torch_geometric pyarrow==15.0.0 gdown && \
+          pip install ipykernel pandas scanpy numba "numpy<2" torchtext==0.17.2 scib "scvi-tools<1.0" datasets==2.14.5 transformers==4.36.2 wandb "cell-gears<0.0.3" torch_geometric pyarrow==15.0.0 gdown && \
           cd scGPT && pip install -e . --no-deps
 
 runners:
diff --git a/src/methods/scgpt_finetuned/script.py b/src/methods/scgpt_finetuned/script.py
index 7123bd33d..dc9b3a40e 100644
--- a/src/methods/scgpt_finetuned/script.py
+++ b/src/methods/scgpt_finetuned/script.py
@@ -227,7 +227,7 @@
     "dropout": 0.2,
     "schedule_ratio": 0.9,  # Learning rate decay
     "log_interval": 100,
-    "fast_transformer": False,  # TODO: Set True if flash-attn is installed
+    "fast_transformer": False,  # requires flash-attn
     "pre_norm": False,
     "amp": True,  # Automatic Mixed Precision
 }
diff --git a/src/methods/scgpt_zeroshot/config.vsh.yaml b/src/methods/scgpt_zeroshot/config.vsh.yaml
index 3ff6425cc..3faf0c5cc 100644
--- a/src/methods/scgpt_zeroshot/config.vsh.yaml
+++ b/src/methods/scgpt_zeroshot/config.vsh.yaml
@@ -51,21 +51,12 @@ resources:
 engines:
   - type: docker
     image: openproblems/base_pytorch_nvidia:1
-    # TODO: Try to find working installation of flash attention (flash-attn<1.0.5)
     setup:
-      #- type: python
-      #  pypi:
-      #    - gdown
-      #    - scgpt # Install from PyPI to get dependencies
-      #- type: docker
-      #  # Force re-installing from GitHub to get bug fixes
-      #  run: pip install --upgrade --no-deps --force-reinstall git+https://github.com/bowang-lab/scGPT.git
       - type: docker
         run: |
           git clone https://github.com/bowang-lab/scGPT && \
           pip install torch==2.2.0 torchvision==0.17.0 torchaudio==2.2.0 --index-url https://download.pytorch.org/whl/cu121 && \
-          pip install "flash-attn<1.0.5" --no-build-isolation && \
-          pip install ipykernel pandas scanpy numba "numpy<1.24" torchtext==0.17.0 scib "scvi-tools<1.0" datasets==2.14.5 transformers==4.33.2 wandb "cell-gears<0.0.3" torch_geometric pyarrow==15.0.0 gdown && \
+          pip install ipykernel pandas scanpy numba "numpy<2" torchtext==0.17.2 scib "scvi-tools<1.0" datasets==2.14.5 transformers==4.36.2 wandb "cell-gears<0.0.3" torch_geometric pyarrow==15.0.0 gdown && \
           cd scGPT && pip install -e . --no-deps
 
 runners: