For compatibility with newer versions of pandas, use items() instead …

.gitignore

@@ -90,3 +90,14 @@ ENV/
 
 # Visual Studio Code configuration
 .vscode
+
+# Cplex installer and installation (generated by install.sh)
+cplex_studio2211.linux_x86_64.bin
+cplex_studio2211/
+
+# # Compass cache, test, and output files (generated by test.sh)
+_tmp/
+expression.tsv
+model.json.gz
+reactions.tsv
+compass/Resources/COMPASS/RECON2_mat/default-media/preprocess.json

compass/compass/algorithm.py

@@ -356,7 +356,7 @@ def compass_exchange(model, problem, reaction_penalties, only_exchange=False, pe
         if(problem.objective.get_name() != 'reaction_penalties'):
             utils.reset_objective(problem)
             problem.objective.set_linear(
-                list(reaction_penalties.iteritems())
+                list(reaction_penalties.items())
             )
             problem.objective.set_name('reaction_penalties')
             problem.objective.set_sense(problem.objective.sense.minimize)
@@ -414,7 +414,7 @@ def compass_exchange(model, problem, reaction_penalties, only_exchange=False, pe
         if(problem.objective.get_name() != 'reaction_penalties'):
             utils.reset_objective(problem)
             problem.objective.set_linear(
-                list(reaction_penalties.iteritems())
+                list(reaction_penalties.items())
             )
             problem.objective.set_name('reaction_penalties')
             problem.objective.set_sense(problem.objective.sense.minimize)
@@ -522,7 +522,7 @@ def compass_reactions(model, problem, reaction_penalties, perf_log=None, args =
             if(problem.objective.get_name() != 'reaction_penalties'):
                 utils.reset_objective(problem)
                 problem.objective.set_linear(
-                    list(reaction_penalties.iteritems())
+                    list(reaction_penalties.items())
                 )
                 problem.objective.set_name('reaction_penalties')
                 problem.objective.set_sense(problem.objective.sense.minimize)

compass/compass/algorithm_t.py

@@ -304,7 +304,7 @@ def compass_transposed(ranges, data, model, media, args):
                 # Minimize Penalty
                 utils.reset_objective(problem)
                 problem.objective.set_linear(
-                    list(reaction_penalties[sample_name].iteritems())
+                    list(reaction_penalties[sample_name].items())
                 )
                 problem.objective.set_sense(problem.objective.sense.minimize)
 

compass/compass/microclustering.py

@@ -98,8 +98,8 @@ def filterGenesThreshold(data, threshold):
 
 def filterGenesFano(data, num_mad=2):
     #Could sample columns at random to improve runtime
-    mu = data.mean(axis=1).ravel()
-    fano = data.var(axis=1).ravel() / mu
+    mu = data.mean(axis=1).to_numpy()
+    fano = data.var(axis=1).to_numpy() / mu
 
     mu_argsort = np.argsort(mu)
     mu_sort = mu[mu_argsort]
@@ -178,7 +178,7 @@ def pool_matrix_cols(data, pools):
         for i in pools[g]:
             groups[data.columns[i]] = g
     groups = pd.DataFrame.from_dict(groups, orient='index', columns=['compass_microcluster']).T
-    return data.append(groups).T.groupby("compass_microcluster").mean().T.rename(mapper=lambda x: 'cluster_'+str(int(x)), axis=1)
+    return pd.concat([data, groups]).T.groupby("compass_microcluster").mean().T.rename(mapper=lambda x: 'cluster_'+str(int(x)), axis=1)
 
 def unpool_columns(pooled_data, pools, data):
     unpooled_cols = []

compass/compass/penalties.py

@@ -155,7 +155,7 @@ def eval_reaction_penalties_shared(model, expression,
     # Compute reaction expression for each sample
 
     reaction_expression = []
-    for name, expression_data in expression.iteritems():
+    for name, expression_data in expression.items():
         reaction_expression.append(
             eval_reaction_expression_single(
                 model, expression_data, and_function

install.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+set -e  # Exit immediately if a command exits with a non-zero status.
+set -u  # Treat unset variables as an error.
+
+# Set the Cplex installer name and the install path for Cplex.
+CPLEX_INSTALLER="cplex_studio2211.linux_x86_64.bin"
+CPLEX_INSTALL_DIR="cplex_studio2211"
+CPLEX_INSTALL_PATH=$(realpath "${CPLEX_INSTALL_DIR}")
+
+# Set up virtual environment.
+python3 -m venv .env
+# shellcheck disable=SC1091
+source .env/bin/activate
+
+# Install Cplex and its Python API.
+chmod u+x "${CPLEX_INSTALLER}"
+"./${CPLEX_INSTALLER}" -i silent -DINSTALLER_UI=silent -DLICENSE_ACCEPTED=TRUE -DUSER_INSTALL_DIR="${CPLEX_INSTALL_PATH}"
+python3 "${CPLEX_INSTALL_PATH}/python/setup.py" install
+
+# Install Compass.
+pip3 install --editable .

test.sh

@@ -0,0 +1,18 @@
+#!/usr/bin/env bash
+
+set -e  # Exit immediately if a command exits with a non-zero status.
+
+# Activate the environment generated by install.sh.
+# shellcheck disable=SC1091
+source .env/bin/activate
+
+# Download the test data.
+gdown https://raw.githubusercontent.com/YosefLab/Compass/refs/heads/master/compass/Resources/Test-Data/tsv_format/expression.tsv
+
+# Run Compass.
+compass --num-thread 32 --data expression.tsv --species homo_sapiens
+
+# Clean up.
+rm expression.tsv
+rm model.json.gz
+rm reactions.tsv