Bug fixes:

* Remove PATH modification from check_pathvar
* Rename check_pathvar to check_system_path
* Add conda_prepend_bin function to handle PATH modification during activation
* Add logic to handle first-run activation, and subsequent calls to change conda environments (otherwise conda clobbers its own shell functions)
* Use $CONDA_PYTHON_EXE and $CONDA_EXE to ensure conda comes from the just-installed tree

1 files changed, 34 insertions, 1 deletions

diff --git a/src/lib/core/conda.c b/src/lib/core/conda.c
index fa3052a..435af35 100644
--- a/src/lib/core/conda.c
+++ b/src/lib/core/conda.c
@@ -207,6 +207,24 @@ int conda_exec(const char *args) {
     return system(command);
 }
 
+static int conda_prepend_bin(const char *root) {
+    const char *system_path_old = getenv("PATH");
+    char conda_bin[PATH_MAX] = {0};
+
+    snprintf(conda_bin, sizeof(conda_bin) - 1, "%s/bin:%s/condabin", root, root);
+
+    if (!strstr(system_path_old, conda_bin)) {
+        // conda_bin is not present in PATH. Add it to the head.
+        char system_path_new[STASIS_BUFSIZ];
+        sprintf(system_path_new, "%s:%s", conda_bin, system_path_old);
+        if (setenv("PATH", system_path_new, 1) < 0) {
+            SYSERROR("Unable to prepend to PATH: %s", conda_bin);
+            return -1;
+        }
+    }
+    return 0;
+}
+
 int conda_activate(const char *root, const char *env_name) {
     FILE *fp = NULL;
     const char *init_script_conda = "/etc/profile.d/conda.sh";
@@ -248,9 +266,24 @@ int conda_activate(const char *root, const char *env_name) {
         return -1;
     }
 
+    if (conda_prepend_bin(root)) {
+        remove(logfile);
+        return -1;
+    }
+
     // Fully activate conda and record its effect on the runtime environment
     char command[PATH_MAX * 3];
-    snprintf(command, sizeof(command) - 1, "set -a; source %s; source %s; conda activate %s &>/dev/null; env -0", path_conda, path_mamba, env_name);
+    const char *conda_shlvl = getenv("CONDA_SHLVL");
+    if (conda_shlvl == NULL || strcmp(conda_shlvl, "0") == 0) {
+        // First-run initialization
+        snprintf(command, sizeof(command) - 1, "source %s; source %s; conda activate %s &>/dev/null; env -0", path_conda, path_mamba, env_name);
+    } else {
+        // Conda is already available and configured.
+        // Make calls directly to conda using conda's base interpreter.
+        // The shell functions generated by sourcing path_conda and path_mamba are extremely inconsistent
+        // in this environment. DO NOT USE THEM.
+        snprintf(command, sizeof(command) - 1, "$CONDA_PYTHON_EXE $CONDA_EXE activate %s &>/dev/null; env -0", env_name);
+    }
     int retval = shell(&proc, command);
     if (retval) {
         // it didn't work; drop out for cleanup