Merge pull request #69 from jhunkeler/workaround-shebang-nightmare

Workaround for shebang nightmare

10 files changed, 188 insertions, 83 deletions

diff --git a/include/conda.h b/include/conda.h
index f031479..b8d0caa 100644
--- a/include/conda.h
+++ b/include/conda.h
@@ -229,4 +229,6 @@ const char *pkg_index_provides_strerror(int code);
 
 char *conda_get_active_environment();
 
+int conda_env_exists(const char *root, const char *name);
+
 #endif //STASIS_CONDA_H
diff --git a/include/utils.h b/include/utils.h
index 4ade817..e26b3c5 100644
--- a/include/utils.h
+++ b/include/utils.h
@@ -392,4 +392,20 @@ int mkdirs(const char *_path, mode_t mode);
  */
 char *find_version_spec(char *package_name);
 
+// mode flags for env_manipulate_pathstr
+#define PM_APPEND 1 << 0
+#define PM_PREPEND 1 << 1
+#define PM_ONCE  1 << 2
+
+/**
+* Add paths to the head or tail of an environment variable.
+*
+* @param key environment variable to manipulate
+* @param path to insert (does not need to exist)
+* @param mode PM_APPEND `$path:$PATH`
+* @param mode PM_PREPEND `$PATH:path`
+* @param mode PM_ONCE do not manipulate if `path` is present in PATH variable
+*/
+int env_manipulate_pathstr(const char *key, char *path, int mode);
+
 #endif //STASIS_UTILS_H
diff --git a/src/cli/stasis/stasis_main.c b/src/cli/stasis/stasis_main.c
index e188b2e..093e32e 100644
--- a/src/cli/stasis/stasis_main.c
+++ b/src/cli/stasis/stasis_main.c
@@ -225,14 +225,6 @@ int main(int argc, char *argv[]) {
         exit(1);
     }
 
-    msg(STASIS_MSG_L1, "Conda setup\n");
-    delivery_get_conda_installer_url(&ctx, installer_url);
-    msg(STASIS_MSG_L2, "Downloading: %s\n", installer_url);
-    if (delivery_get_conda_installer(&ctx, installer_url)) {
-        msg(STASIS_MSG_ERROR, "download failed: %s\n", installer_url);
-        exit(1);
-    }
-
     // Unlikely to occur: this should help prevent rmtree() from destroying your entire filesystem
     // if path is "/" then, die
     // or if empty string, die
@@ -241,6 +233,30 @@ int main(int argc, char *argv[]) {
         exit(1);
     }
 
+    // 2 = #!
+    // 5 = /bin\n
+    const size_t prefix_len = strlen(ctx.storage.conda_install_prefix) + 2 + 5;
+    const size_t prefix_len_max = 127;
+    msg(STASIS_MSG_L1, "Checking length of conda installation prefix\n");
+    if (!strcmp(ctx.system.platform[DELIVERY_PLATFORM], "Linux") && prefix_len > prefix_len_max) {
+        msg(STASIS_MSG_L2 | STASIS_MSG_ERROR,
+            "The shebang, '#!%s/bin/python\\n' is too long (%zu > %zu).\n",
+            ctx.storage.conda_install_prefix, prefix_len, prefix_len_max);
+        msg(STASIS_MSG_L2 | STASIS_MSG_ERROR,
+            "Conda's workaround to handle long path names does not work consistently within STASIS.\n");
+        msg(STASIS_MSG_L2 | STASIS_MSG_ERROR,
+            "Please try again from a different, \"shorter\", directory.\n");
+        exit(1);
+    }
+
+    msg(STASIS_MSG_L1, "Conda setup\n");
+    delivery_get_conda_installer_url(&ctx, installer_url);
+    msg(STASIS_MSG_L2, "Downloading: %s\n", installer_url);
+    if (delivery_get_conda_installer(&ctx, installer_url)) {
+        msg(STASIS_MSG_ERROR, "download failed: %s\n", installer_url);
+        exit(1);
+    }
+
     msg(STASIS_MSG_L2, "Installing: %s\n", ctx.conda.installer_name);
     delivery_install_conda(ctx.conda.installer_path, ctx.storage.conda_install_prefix);
 
@@ -294,7 +310,7 @@ int main(int argc, char *argv[]) {
     }
 
     if (!isempty(ctx.meta.based_on)) {
-        if (conda_env_remove(env_name)) {
+        if (conda_env_exists(ctx.storage.conda_install_prefix, env_name) && conda_env_remove(env_name)) {
             msg(STASIS_MSG_ERROR | STASIS_MSG_L2, "failed to remove release environment: %s\n", env_name);
             exit(1);
         }
@@ -305,7 +321,7 @@ int main(int argc, char *argv[]) {
             exit(1);
         }
 
-        if (conda_env_remove(env_name_testing)) {
+        if (conda_env_exists(ctx.storage.conda_install_prefix, env_name_testing) && conda_env_remove(env_name_testing)) {
             msg(STASIS_MSG_ERROR | STASIS_MSG_L2, "failed to remove testing environment %s\n", env_name_testing);
             exit(1);
         }
diff --git a/src/lib/core/conda.c b/src/lib/core/conda.c
index 435af35..b2caa63f 100644
--- a/src/lib/core/conda.c
+++ b/src/lib/core/conda.c
@@ -208,25 +208,70 @@ int conda_exec(const char *args) {
 }
 
 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);
+    snprintf(conda_bin, sizeof(conda_bin) - 1, "%s/bin", root);
+    if (env_manipulate_pathstr("PATH", conda_bin, PM_PREPEND | PM_ONCE)) {
+        return -1;
+    }
+    return 0;
+}
 
-    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);
+static int conda_prepend_condabin(const char *root) {
+    char conda_condabin[PATH_MAX] = {0};
+
+    snprintf(conda_condabin, sizeof(conda_condabin) - 1, "%s/condabin", root);
+    if (env_manipulate_pathstr("PATH", conda_condabin, PM_PREPEND | PM_ONCE)) {
+        return -1;
+    }
+    return 0;
+}
+
+static int env0_to_runtime(const char *logfile) {
+    FILE *fp = fopen(logfile, "r");
+    if (!fp) {
+        perror(logfile);
+        return -1;
+    }
+
+    while (!feof(fp)) {
+        char buf[STASIS_BUFSIZ] = {0};
+        int ch = 0;
+        size_t z = 0;
+        // We are ingesting output from "env -0" and can't use fgets()
+        // Copy each character into the buffer until we encounter '\0' or EOF
+        while (z < sizeof(buf) && (ch = (int) fgetc(fp)) != 0) {
+            if (ch == EOF) {
+                break;
+            }
+            buf[z] = (char) ch;
+            z++;
+        }
+        buf[strlen(buf)] = 0;
+
+        if (!strlen(buf)) {
+            continue;
+        }
+
+        char **part = split(buf, "=", 1);
+        if (!part) {
+            perror("unable to split environment variable buffer");
             return -1;
         }
+        if (!part[0]) {
+            msg(STASIS_MSG_WARN | STASIS_MSG_L1, "Invalid environment variable key ignored: '%s'\n", buf);
+        } else if (!part[1]) {
+            msg(STASIS_MSG_WARN | STASIS_MSG_L1, "Invalid environment variable value ignored: '%s'\n", buf);
+        } else {
+            setenv(part[0], part[1], 1);
+        }
+        GENERIC_ARRAY_FREE(part);
     }
+    fclose(fp);
     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";
     const char *init_script_mamba = "/etc/profile.d/mamba.sh";
     char path_conda[PATH_MAX] = {0};
@@ -266,24 +311,42 @@ int conda_activate(const char *root, const char *env_name) {
         return -1;
     }
 
-    if (conda_prepend_bin(root)) {
+    // Fully activate conda and record its effect on the runtime environment
+    char command[PATH_MAX * 3];
+    const char *conda_shlvl_str = getenv("CONDA_SHLVL");
+    unsigned long conda_shlvl = 0;
+    if (conda_shlvl_str) {
+        conda_shlvl = strtol(conda_shlvl_str, NULL, 10);
+    }
+
+    if (conda_prepend_condabin(root)) {
         remove(logfile);
         return -1;
     }
 
-    // Fully activate conda and record its effect on the runtime environment
-    char command[PATH_MAX * 3];
-    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 $CONDA_EXE activate %s &>/dev/null; env -0", env_name);
+    if (conda_prepend_bin(root)) {
+        remove(logfile);
+        return -1;
     }
+
+    snprintf(command, sizeof(command) - 1,
+        "set -a\n"
+        "source %s\n"
+        "__conda_exe() (\n"
+        "    \"$CONDA_PYTHON_EXE\" \"$CONDA_EXE\" $_CE_M $_CE_CONDA \"$@\"\n"
+        ")\n\n"
+        "export -f __conda_exe\n"
+        "source %s\n"
+        "__mamba_exe() (\n"
+        "    \\local MAMBA_CONDA_EXE_BACKUP=$CONDA_EXE\n"
+        "    \\local MAMBA_EXE=$(\\dirname \"${CONDA_EXE}\")/mamba\n"
+        "    \"$CONDA_PYTHON_EXE\" \"$MAMBA_EXE\" $_CE_M $_CE_CONDA \"$@\"\n"
+        ")\n\n"
+        "export -f __mamba_exe\n"
+        "%s\n"
+        "conda activate %s 1>&2\n"
+        "env -0\n", path_conda, path_mamba, conda_shlvl ? "conda deactivate" : ":", env_name);
+
     int retval = shell(&proc, command);
     if (retval) {
         // it didn't work; drop out for cleanup
@@ -294,47 +357,9 @@ int conda_activate(const char *root, const char *env_name) {
     // Parse the log file:
     // 1. Extract the environment keys and values from the sub-shell
     // 2. Apply it to STASIS's runtime environment
-    // 3. Now we're ready to execute conda commands anywhere
-    fp = fopen(proc.f_stdout, "r");
-    if (!fp) {
-        perror(logfile);
+    if (env0_to_runtime(logfile) < 0) {
         return -1;
     }
-
-    while (!feof(fp)) {
-        char buf[STASIS_BUFSIZ] = {0};
-        int ch = 0;
-        size_t z = 0;
-        // We are ingesting output from "env -0" and can't use fgets()
-        // Copy each character into the buffer until we encounter '\0' or EOF
-        while (z < sizeof(buf) && (ch = (int) fgetc(fp)) != 0) {
-            if (ch == EOF) {
-                break;
-            }
-            buf[z] = (char) ch;
-            z++;
-        }
-        buf[strlen(buf)] = 0;
-
-        if (!strlen(buf)) {
-            continue;
-        }
-
-        char **part = split(buf, "=", 1);
-        if (!part) {
-            perror("unable to split environment variable buffer");
-            return -1;
-        }
-        if (!part[0]) {
-            msg(STASIS_MSG_WARN | STASIS_MSG_L1, "Invalid environment variable key ignored: '%s'\n", buf);
-        } else if (!part[1]) {
-            msg(STASIS_MSG_WARN | STASIS_MSG_L1, "Invalid environment variable value ignored: '%s'\n", buf);
-        } else {
-            setenv(part[0], part[1], 1);
-        }
-        GENERIC_ARRAY_FREE(part);
-    }
-    fclose(fp);
     remove(logfile);
     return 0;
 }
@@ -346,7 +371,6 @@ int conda_check_required() {
     const char *conda_minimum_viable_tools[] = {
             "boa",
             "conda-build",
-            "conda-verify",
             NULL
     };
 
@@ -518,3 +542,9 @@ int conda_index(const char *path) {
     sprintf(command, "index %s", path);
     return conda_exec(command);
 }
+
+int conda_env_exists(const char *root, const char *name) {
+    char path[PATH_MAX] = {0};
+    snprintf(path, sizeof(path) - 1 - 6, "%s/envs/%s", root, name);
+    return access(path, F_OK) == 0;
+}
diff --git a/src/lib/core/utils.c b/src/lib/core/utils.c
index 5f0807c..18731e6 100644
--- a/src/lib/core/utils.c
+++ b/src/lib/core/utils.c
@@ -808,3 +808,45 @@ int mkdirs(const char *_path, mode_t mode) {
 char *find_version_spec(char *str) {
     return strpbrk(str, "@~=<>!");
 }
+
+int env_manipulate_pathstr(const char *key, char *path, int mode) {
+    if (isempty(path)) {
+        SYSERROR("%s", "New PATH element cannot be zero-length or NULL");
+        return -1;
+    }
+
+    const char *system_path_old = getenv("PATH");
+    if (!system_path_old) {
+        SYSERROR("%s", "Unable to read PATH");
+        return -1;
+    }
+
+    char *system_path_new = NULL;
+
+    if (mode & PM_APPEND) {
+        asprintf(&system_path_new, "%s%s%s", system_path_old, PATH_SEP, path);
+    } else if (mode & PM_PREPEND) {
+        asprintf(&system_path_new, "%s%s%s", path, PATH_SEP, system_path_old);
+    }
+
+    if (!system_path_new) {
+        SYSERROR("%s", "Unable to allocate memory to update PATH");
+        return -1;
+    }
+
+    if (mode & PM_ONCE) {
+        if (!strstr(system_path_old, path)) {
+            guard_free(system_path_new);
+            return 0;
+        }
+    }
+    if (setenv(key, system_path_new, 1) < 0) {
+        SYSERROR("Unable to %s to PATH: %s", mode & PM_APPEND ? "append" : "prepend", path);
+        guard_free(system_path_new);
+        return -1;
+    }
+
+    guard_free(system_path_new);
+    return 0;
+}
+
diff --git a/stasis.ini b/stasis.ini
index ba3331a..043fcec 100644
--- a/stasis.ini
+++ b/stasis.ini
@@ -18,7 +18,6 @@ conda_fresh_start = true
 conda_packages =
     conda-build>=3.22.0
     boa
-    conda-verify
     conda-libmamba-solver
 
 ; (list) Python packages to be installed/overridden in the base environment
diff --git a/tests/data/generic_based_on.ini b/tests/data/gbo.ini
index 1287933..609b8f3 100644
--- a/tests/data/generic_based_on.ini
+++ b/tests/data/gbo.ini
@@ -1,10 +1,10 @@
 [meta]
 mission = generic
-name = GENERIC_BASED_ON
+name = GBO
 version = 1.2.3
 rc = 1
 final = false
-based_on = {{ env:TEST_DATA }}/generic_based_on.yml
+based_on = {{ env:TEST_DATA }}/gbo.yml
 python = 3.11
 
 
diff --git a/tests/data/generic_based_on.yml b/tests/data/gbo.yml
index 3ab97a7..3ab97a7 100644
--- a/tests/data/generic_based_on.yml
+++ b/tests/data/gbo.yml
diff --git a/tests/rt_generic_based_on.sh b/tests/rt_generic_based_on.sh
index 7d78399..08498be 100644
--- a/tests/rt_generic_based_on.sh
+++ b/tests/rt_generic_based_on.sh
@@ -2,7 +2,7 @@
 here="$(dirname ${BASH_SOURCE[0]})"
 source $here/setup.sh
 
-TEST_NAME=generic_based_on
+TEST_NAME=gbo
 PYTHON_VERSIONS=(
     3.11
 )
diff --git a/tests/setup.sh b/tests/setup.sh
index 50209ae..7e38cf9 100644
--- a/tests/setup.sh
+++ b/tests/setup.sh
@@ -32,7 +32,7 @@ popd() {
     command popd 1>/dev/null
 }
 
-WS_DEFAULT="workspaces/rt_workspace_"
+WS_DEFAULT="ws/_"
 setup_workspace() {
     if [ -z "$1" ]; then
         echo "setup_workspace requires a name argument" >&2
@@ -46,8 +46,8 @@ setup_workspace() {
     fi
     WORKSPACE="$(realpath $WORKSPACE)"
     
-    export PREFIX="$WORKSPACE"/local
-    if ! mkdir -p "$PREFIX"; then
+    export INSTALL_DIR="$WORKSPACE"/local
+    if ! mkdir -p "$INSTALL_DIR"; then
         echo "directory creation failed. cannot continue" >&2
         return 1;
     fi
@@ -78,7 +78,7 @@ teardown_workspace() {
 
 install_stasis() {
     pushd "$BUILD_DIR"
-    if ! cmake -DCMAKE_INSTALL_PREFIX="$PREFIX" -DCMAKE_BUILD_TYPE=Debug "${TOPDIR}"/../..; then
+    if ! cmake -DCMAKE_INSTALL_PREFIX="$INSTALL_DIR" -DCMAKE_BUILD_TYPE=Debug "${TOPDIR}"/../..; then
         echo "cmake failed" >&2
         return 1
     fi
@@ -88,7 +88,7 @@ install_stasis() {
         return 1
     fi
 
-    export PATH="$PREFIX/bin:$PATH"
+    export PATH="$INSTALL_DIR/bin:$PATH"
     hash -r
     if ! type -P stasis; then
         echo "stasis program not on PATH" >&2
@@ -120,7 +120,7 @@ run_command() {
             (( STASIS_TEST_RESULT_SKIP++ ))
         else
             echo "... FAIL"
-            if (( $(wc -c "$logfile" | cut -d ' ' -f 1) > 1 )); then
+            if [[ -s "$logfile" ]]; then
                 echo "#"
                 echo "# Last $lines_on_error line(s) follow:"
                 echo "#"
@@ -282,4 +282,4 @@ clean_up() {
     else
         exit 0
     fi
-}
\ No newline at end of file
+}