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

4 files changed, 38 insertions, 9 deletions

diff --git a/src/cli/stasis/stasis_main.c b/src/cli/stasis/stasis_main.c
index cda5fa6..e188b2e 100644
--- a/src/cli/stasis/stasis_main.c
+++ b/src/cli/stasis/stasis_main.c
@@ -133,6 +133,8 @@ int main(int argc, char *argv[]) {
 
     printf(BANNER, VERSION, AUTHOR);
 
+    check_system_path();
+
     msg(STASIS_MSG_L1, "Setup\n");
 
     tpl_setup_vars(&ctx);
@@ -241,7 +243,6 @@ int main(int argc, char *argv[]) {
 
     msg(STASIS_MSG_L2, "Installing: %s\n", ctx.conda.installer_name);
     delivery_install_conda(ctx.conda.installer_path, ctx.storage.conda_install_prefix);
-    check_pathvar(&ctx);
 
     msg(STASIS_MSG_L2, "Configuring: %s\n", ctx.storage.conda_install_prefix);
     delivery_conda_enable(&ctx, ctx.storage.conda_install_prefix);
diff --git a/src/cli/stasis/system_requirements.c b/src/cli/stasis/system_requirements.c
index 53ebbf7..d8d7df3 100644
--- a/src/cli/stasis/system_requirements.c
+++ b/src/cli/stasis/system_requirements.c
@@ -67,16 +67,11 @@ void check_requirements(struct Delivery *ctx) {
     check_system_env_requirements();
 }
 
-void check_pathvar(struct Delivery *ctx) {
+void check_system_path() {
     char *pathvar = NULL;
     pathvar = getenv("PATH");
     if (!pathvar) {
         msg(STASIS_MSG_ERROR | STASIS_MSG_L2, "PATH variable is not set. Cannot continue.\n");
         exit(1);
-    } else {
-        char pathvar_tmp[STASIS_BUFSIZ];
-        sprintf(pathvar_tmp, "%s/bin:%s", ctx->storage.conda_install_prefix, pathvar);
-        setenv("PATH", pathvar_tmp, 1);
-        pathvar = NULL;
     }
 }
\ No newline at end of file
diff --git a/src/cli/stasis/system_requirements.h b/src/cli/stasis/system_requirements.h
index 3a6fa25..ddc2705 100644
--- a/src/cli/stasis/system_requirements.h
+++ b/src/cli/stasis/system_requirements.h
@@ -5,9 +5,9 @@
 #include "callbacks.h"
 #include "envctl.h"
 
+void check_system_path();
 void check_system_env_requirements();
 void check_system_requirements(struct Delivery *ctx);
 void check_requirements(struct Delivery *ctx);
-void check_pathvar(struct Delivery *ctx);
 
 #endif //STASIS_SYSTEM_REQUIREMENTS_H
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