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chore: use dsub fork#485

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chore: use dsub fork#485
agitter wants to merge 1 commit into
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@agitter agitter commented Jun 11, 2026

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Closes #475
Related to #470 (comment)

@agitter

agitter commented Jun 11, 2026

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I confirmed this resolves the tenacity dependency version conflict in a fresh Codespace install.

@agitter agitter requested a review from ntalluri June 12, 2026 21:50
@agitter agitter mentioned this pull request Jun 16, 2026
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@agitter

agitter commented Jun 19, 2026

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@ntalluri can you please review and merge once you confirm this fixes the error? The relevant part of the build log from the GitHub actions test is below.

6s
Run pip install .
Processing /home/runner/work/spras/spras
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting adjusttext==0.7.3 (from spras==0.6.0)
  Downloading adjustText-0.7.3.tar.gz (7.5 kB)
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting snakemake==9.6.2 (from spras==0.6.0)
  Downloading snakemake-9.6.2-py3-none-any.whl.metadata (2.6 kB)
Requirement already satisfied: docker==7.1.0 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from spras==0.6.0) (7.1.0)
Requirement already satisfied: matplotlib==3.10.3 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from spras==0.6.0) (3.10.3)
Requirement already satisfied: networkx==3.5 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from spras==0.6.0) (3.5)
Requirement already satisfied: pandas==2.3.0 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from spras==0.6.0) (2.3.0)
Requirement already satisfied: pydantic==2.11.7 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from spras==0.6.0) (2.11.7)
Requirement already satisfied: numpy==2.3.1 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from spras==0.6.0) (2.3.1)
Requirement already satisfied: requests==2.32.4 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from spras==0.6.0) (2.32.4)
Requirement already satisfied: scikit-learn==1.7.0 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from spras==0.6.0) (1.7.0)
Requirement already satisfied: seaborn==0.13.2 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from spras==0.6.0) (0.13.2)
Requirement already satisfied: spython==0.3.14 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from spras==0.6.0) (0.3.14)
Requirement already satisfied: pip==25.3 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from spras==0.6.0) (25.3)
Requirement already satisfied: urllib3>=1.26.0 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from docker==7.1.0->spras==0.6.0) (2.7.0)
Requirement already satisfied: contourpy>=1.0.1 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from matplotlib==3.10.3->spras==0.6.0) (1.3.3)
Requirement already satisfied: cycler>=0.10 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from matplotlib==3.10.3->spras==0.6.0) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from matplotlib==3.10.3->spras==0.6.0) (4.63.0)
Requirement already satisfied: kiwisolver>=1.3.1 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from matplotlib==3.10.3->spras==0.6.0) (1.5.0)
Requirement already satisfied: packaging>=20.0 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from matplotlib==3.10.3->spras==0.6.0) (26.2)
Requirement already satisfied: pillow>=8 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from matplotlib==3.10.3->spras==0.6.0) (12.2.0)
Requirement already satisfied: pyparsing>=2.3.1 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from matplotlib==3.10.3->spras==0.6.0) (3.3.2)
Requirement already satisfied: python-dateutil>=2.7 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from matplotlib==3.10.3->spras==0.6.0) (2.9.0)
Requirement already satisfied: pytz>=2020.1 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from pandas==2.3.0->spras==0.6.0) (2025.2)
Requirement already satisfied: tzdata>=2022.7 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from pandas==2.3.0->spras==0.6.0) (2026.2)
Requirement already satisfied: annotated-types>=0.6.0 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from pydantic==2.11.7->spras==0.6.0) (0.7.0)
Requirement already satisfied: pydantic-core==2.33.2 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from pydantic==2.11.7->spras==0.6.0) (2.33.2)
Requirement already satisfied: typing-extensions>=4.12.2 in /usr/share/miniconda3/envs/spras/lib/python3.11/site-packages (from pydantic==2.11.7->spras==0.6.0) (4.15.0)
Downloading snakemake-9.6.2-py3-none-any.whl (1.1 MB)
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 27.3 MB/s  0:00:00
Downloading packaging-25.0-py3-none-any.whl (66 kB)
Downloading tenacity-9.1.4-py3-none-any.whl (28 kB)
Building wheels for collected packages: spras, adjusttext
  Building wheel for spras (pyproject.toml): started
  Building wheel for spras (pyproject.toml): finished with status 'done'
  Created wheel for spras: filename=spras-0.6.0-py3-none-any.whl size=96258 sha256=8508e43fdf26074675c5191db065c8a01b527efb2dd9ed0b3e0f78c3be913f6f
  Stored in directory: /tmp/pip-ephem-wheel-cache-ugfbll93/wheels/55/f4/67/88ea12dbac4c2ae8b219401d01f4e18b9fa96d9512b177051a
  Building wheel for adjusttext (pyproject.toml): started
  Building wheel for adjusttext (pyproject.toml): finished with status 'done'
  Created wheel for adjusttext: filename=adjusttext-0.7.3-py3-none-any.whl size=7104 sha256=6b7e0adeea0638f41091f24c28d570deddccdd8fe9ff69627d2ad268b278a780
  Stored in directory: /home/runner/.cache/pip/wheels/b8/d7/64/61c5eaf7241aa051154af0d4b03810653b987f1dd24ccfd193
Successfully built spras adjusttext
Installing collected packages: tenacity, packaging, adjusttext, snakemake, spras
  Attempting uninstall: tenacity
    Found existing installation: tenacity 9.1.2
    Uninstalling tenacity-9.1.2:
      Successfully uninstalled tenacity-9.1.2
  Attempting uninstall: packaging
    Found existing installation: packaging 26.2
    Uninstalling packaging-26.2:
      Successfully uninstalled packaging-26.2
  Attempting uninstall: adjusttext
    Found existing installation: adjustText 1.3.0
    Uninstalling adjustText-1.3.0:
      Successfully uninstalled adjustText-1.3.0
  Attempting uninstall: snakemake
    Found existing installation: snakemake 0.0.0
    Uninstalling snakemake-0.0.0:
      Successfully uninstalled snakemake-0.0.0

Successfully installed adjusttext-0.7.3 packaging-25.0 snakemake-9.6.2 spras-0.6.0 tenacity-9.1.4

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@ntalluri ntalluri Awaiting requested review from ntalluri

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pip dependency conflict

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