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Address CI failures #262

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merged 4 commits into from
Dec 2, 2024
Merged

Address CI failures #262

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6ee2172
Force overwrite existing Apptainer image
thalassemia Dec 2, 2024
0a3ceb7
Use hvplot backend
thalassemia Dec 2, 2024
f3fd041
Add mypy to requirements
thalassemia Dec 2, 2024
3979b89
Ignore mypy errors
thalassemia Dec 2, 2024
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4 changes: 2 additions & 2 deletions ecoli/analysis/multigeneration/new_gene_counts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -94,15 +94,15 @@ def plot(
)

# mRNA counts
mrna_plot = new_gene_data.plot.line(
mrna_plot = new_gene_data.hvplot.line( # type: ignore[attr-defined]
x="Time (min)",
y=new_gene_mRNA_ids,
ylabel="mRNA Counts",
title="New Gene mRNA Counts",
)

# Protein counts
protein_plot = new_gene_data.plot.line(
protein_plot = new_gene_data.hvplot.line( # type: ignore[attr-defined]
x="Time (min)",
y=new_gene_monomer_ids,
ylabel="Protein Counts",
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2 changes: 1 addition & 1 deletion ecoli/analysis/single/mass_fraction_summary.py
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Expand Up @@ -63,7 +63,7 @@ def plot(
},
}
mass_fold_change = pl.DataFrame(new_columns)
plot_namespace = mass_fold_change.plot
plot_namespace = mass_fold_change.hvplot # type: ignore[attr-defined]
# hvplot.output(backend='matplotlib')
plotted_data = plot_namespace.line(
x="Time (min)",
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4 changes: 3 additions & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# Note: Core required packages are numpy, scipy, biopython, cvxpy, cython, dill,
# duckdb, ete3, gcsfs, pyarrow, hvplot, ipdb, ipython, jupyter, line-profiler, altair,
# numba, orjson, ortools, pandas, polars, pymunk, pytest, pytest-cov, scikit-image,
# scikit-learn, seaborn, swiglpk, sympy, tqdm, unum, jax, vivarium-core, pysal,
# scikit-learn, seaborn, swiglpk, sympy, tqdm, unum, jax, vivarium-core, pysal, mypy,
# opencv-python-headless, statsmodels, ruff, ecos, nbclassic, stochastic-arrow,
# matplotlib, pyqt5, and iteround. Other packages are dependencies of the above.

Expand Down Expand Up @@ -128,6 +128,8 @@ ml_dtypes==0.5.0
momepy==0.9.1
mpmath==1.3.0
multidict==6.1.0
mypy==1.13.0
mypy-extensions==1.0.0
narwhals==1.15.1
nbclassic==1.1.0
nbclient==0.10.1
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2 changes: 1 addition & 1 deletion runscripts/container/build-runtime.sh
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Expand Up @@ -40,7 +40,7 @@ if (( $RUN_LOCAL )); then
docker build -f runscripts/container/runtime/Dockerfile -t "${RUNTIME_IMAGE}" .
elif (( $BUILD_APPTAINER )); then
echo "=== Building WCM runtime Apptainer Image: ${RUNTIME_IMAGE} ==="
apptainer build ${RUNTIME_IMAGE} runscripts/container/runtime/Singularity
apptainer build --force ${RUNTIME_IMAGE} runscripts/container/runtime/Singularity
else
echo "=== Cloud-building WCM runtime Docker Image: ${RUNTIME_IMAGE} ==="
# For this script to work on a Compute Engine VM, you must
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