Merge pull request #262 from CovertLab/tweaks

Address CI failures
CovertLab · Dec 2, 2024 · e888cff · e888cff
2 parents 6a295ba + 3979b89
commit e888cff
Show file tree

Hide file tree

Showing 4 changed files with 7 additions and 5 deletions.
diff --git a/ecoli/analysis/multigeneration/new_gene_counts.py b/ecoli/analysis/multigeneration/new_gene_counts.py
@@ -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",

diff --git a/ecoli/analysis/single/mass_fraction_summary.py b/ecoli/analysis/single/mass_fraction_summary.py
@@ -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)",

diff --git a/requirements.txt b/requirements.txt
@@ -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.
 
@@ -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

diff --git a/runscripts/container/build-runtime.sh b/runscripts/container/build-runtime.sh
@@ -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