two enivronment management

Author: ncborcherding

R/basilisk.R

@@ -1,13 +1,18 @@
 # Bioconductor-compliant management of Python environments
 #
-# This script defines a basilisk environment for immlynx.
+# This script defines basilisk environments for immLynx.
 #
-# The environment is defined using the BasiliskEnvironment function, which
-# specifies the name of the environment, the package name, and the list of
-# required Python packages.
+# Two separate environments are used so that installation failures in
+# problematic packages (soNNia and clusTCR) do not prevent the rest of
+# the Python tooling from working.
 #
-# The defined environment is then used in the wrapper functions to execute
-# Python code using basiliskRun.
+#   immLynxEnv      -- stable dependencies used by the majority of the
+#                      package: OLGA, tcrdist3, metaclonotypist,
+#                      transformers/torch (ESM-2 embeddings), etc.
+#
+#   immLynxExtraEnv -- packages that have historically had installation
+#                      issues: soNNia and clusTCR.  Used only by
+#                      calculate.sonia() and calculate.clustcr().
 #
 # Note: Version checking is disabled because clusTCR is installed directly
 # from its GitHub repository via a git+https:// URL in the `pip` vector,
@@ -17,6 +22,9 @@
 
 basilisk::setBasiliskCheckVersions(FALSE)
 
+# ---------------------------------------------------------------------------
+# Core environment -- stable packages
+# ---------------------------------------------------------------------------
 immLynxEnv <- basilisk::BasiliskEnvironment(
     envname = "immLynxEnv",
     pkgname = "immLynx",
@@ -29,17 +37,35 @@ immLynxEnv <- basilisk::BasiliskEnvironment(
         "scikit-learn=1.1.3",
         "statsmodels=0.13.2",
         "seaborn=0.12.1",
-        "markov-clustering=0.0.6.dev0",
         "faiss-cpu=1.7.4"
     ),
     pip = c(
         "tcrdist3==0.2.2",
         "olga==1.2.4",
-        "sonnia==0.2.5",
         "metaclonotypist==0.2.0",
         "pyrepseq==1.5.1",
         "torch==2.1.2",
-        "transformers==4.36.2",
+        "transformers==4.36.2"
+    )
+)
+
+# ---------------------------------------------------------------------------
+# Extra environment -- soNNia + clusTCR (may fail to install)
+# ---------------------------------------------------------------------------
+immLynxExtraEnv <- basilisk::BasiliskEnvironment(
+    envname = "immLynxExtraEnv",
+    pkgname = "immLynx",
+    packages = c(
+        "python=3.9",
+        "numpy=1.23.4",
+        "scipy=1.8.0",
+        "pandas=1.4.4",
+        "scikit-learn=1.1.3",
+        "markov-clustering=0.0.6.dev0"
+    ),
+    pip = c(
+        "olga==1.2.4",
+        "sonnia==0.2.5",
         "git+https://github.com/svalkiers/clusTCR.git@1.0.3"
     )
 )

R/calculate_helpers.R

@@ -89,7 +89,7 @@ calculate.clustcr <- function(sequences,
                               eps = 0.5,
                               min_samples = 2) {
 
-  proc <- basilisk::basiliskStart(immLynxEnv)
+  proc <- basilisk::basiliskStart(immLynxExtraEnv)
   on.exit(basilisk::basiliskStop(proc))
 
   cluster_df <- basilisk::basiliskRun(proc, function(sequences,
@@ -258,7 +258,7 @@ calculate.sonia <- function(data_folder,
                             n_epochs = 100,
                             save_folder = "sonia_output") {
 
-  proc <- basilisk::basiliskStart(immLynxEnv)
+  proc <- basilisk::basiliskStart(immLynxExtraEnv)
   on.exit(basilisk::basiliskStop(proc))
 
   # Read and prepare data as lists of lists: [[cdr3, v_gene, j_gene], ...]

tests/testthat/helper-immLynx.R

@@ -130,7 +130,7 @@ olga_available <- function() {
 clustcr_available <- function() {
   if (is.null(.module_cache$clustcr)) {
     .module_cache$clustcr <- tryCatch({
-      proc <- basilisk::basiliskStart(immLynx:::immLynxEnv)
+      proc <- basilisk::basiliskStart(immLynx:::immLynxExtraEnv)
       on.exit(basilisk::basiliskStop(proc))
       basilisk::basiliskRun(proc, function() {
         reticulate::import("clustcr")
@@ -145,7 +145,7 @@ clustcr_available <- function() {
 sonnia_available <- function() {
   if (is.null(.module_cache$sonnia)) {
     .module_cache$sonnia <- tryCatch({
-      proc <- basilisk::basiliskStart(immLynx:::immLynxEnv)
+      proc <- basilisk::basiliskStart(immLynx:::immLynxExtraEnv)
       on.exit(basilisk::basiliskStop(proc))
       basilisk::basiliskRun(proc, function() {
         reticulate::import("sonnia.sonnia")