Refactor directory structure

* Move core library sources into src/lib/core
* Move command-line programs into src/cli

1 files changed, 0 insertions, 466 deletions

diff --git a/src/conda.c b/src/conda.c
deleted file mode 100644
index e60abc7..0000000
--- a/src/conda.c
+++ /dev/null
@@ -1,466 +0,0 @@
-//
-// Created by jhunk on 5/14/23.
-//
-
-#include <unistd.h>
-#include "conda.h"
-
-int micromamba(struct MicromambaInfo *info, char *command, ...) {
-    struct utsname sys;
-    uname(&sys);
-
-    tolower_s(sys.sysname);
-    if (!strcmp(sys.sysname, "darwin")) {
-        strcpy(sys.sysname, "osx");
-    }
-
-    if (!strcmp(sys.machine, "x86_64")) {
-        strcpy(sys.machine, "64");
-    }
-
-    char url[PATH_MAX];
-    sprintf(url, "https://micro.mamba.pm/api/micromamba/%s-%s/latest", sys.sysname, sys.machine);
-
-    char installer_path[PATH_MAX];
-    sprintf(installer_path, "%s/latest", getenv("TMPDIR") ? getenv("TMPDIR") : "/tmp");
-
-    if (access(installer_path, F_OK)) {
-        download(url, installer_path, NULL);
-    }
-
-    char mmbin[PATH_MAX];
-    sprintf(mmbin, "%s/micromamba", info->micromamba_prefix);
-
-    if (access(mmbin, F_OK)) {
-        char untarcmd[PATH_MAX * 2];
-        mkdirs(info->micromamba_prefix, 0755);
-        sprintf(untarcmd, "tar -xvf %s -C %s --strip-components=1 bin/micromamba 1>/dev/null", installer_path, info->micromamba_prefix);
-        int untarcmd_status = system(untarcmd);
-        if (untarcmd_status) {
-            return -1;
-        }
-    }
-
-    char cmd[STASIS_BUFSIZ];
-    memset(cmd, 0, sizeof(cmd));
-    sprintf(cmd, "%s -r %s -p %s ", mmbin, info->conda_prefix, info->conda_prefix);
-    va_list args;
-    va_start(args, command);
-    vsprintf(cmd + strlen(cmd), command, args);
-    va_end(args);
-
-    mkdirs(info->conda_prefix, 0755);
-
-    char rcpath[PATH_MAX];
-    sprintf(rcpath, "%s/.condarc", info->conda_prefix);
-    touch(rcpath);
-
-    setenv("CONDARC", rcpath, 1);
-    setenv("MAMBA_ROOT_PREFIX", info->conda_prefix, 1);
-    int status = system(cmd);
-    unsetenv("MAMBA_ROOT_PREFIX");
-
-    return status;
-}
-
-int python_exec(const char *args) {
-    char command[PATH_MAX];
-    memset(command, 0, sizeof(command));
-    snprintf(command, sizeof(command) - 1, "python %s", args);
-    msg(STASIS_MSG_L3, "Executing: %s\n", command);
-    return system(command);
-}
-
-int pip_exec(const char *args) {
-    char command[PATH_MAX];
-    memset(command, 0, sizeof(command));
-    snprintf(command, sizeof(command) - 1, "python -m pip %s", args);
-    msg(STASIS_MSG_L3, "Executing: %s\n", command);
-    return system(command);
-}
-
-int pip_index_provides(const char *index_url, const char *spec) {
-    char cmd[PATH_MAX] = {0};
-    char spec_local[255] = {0};
-
-    if (isempty((char *) spec)) {
-        // NULL or zero-length; no package spec means there's nothing to do.
-        return -1;
-    }
-
-    // Normalize the local spec string
-    strncpy(spec_local, spec, sizeof(spec_local) - 1);
-    tolower_s(spec_local);
-    lstrip(spec_local);
-    strip(spec_local);
-
-    char logfile[] = "/tmp/STASIS-package_exists.XXXXXX";
-    int logfd = mkstemp(logfile);
-    if (logfd < 0) {
-        perror(logfile);
-        remove(logfile);  // fail harmlessly if not present
-        return -1;
-    }
-
-
-    int status = 0;
-    struct Process proc;
-    memset(&proc, 0, sizeof(proc));
-    proc.redirect_stderr = 1;
-    strcpy(proc.f_stdout, logfile);
-
-    // Do an installation in dry-run mode to see if the package exists in the given index.
-    snprintf(cmd, sizeof(cmd) - 1, "python -m pip install --dry-run --no-deps --index-url=%s %s", index_url, spec_local);
-    status = shell(&proc, cmd);
-
-    // Print errors only when shell() itself throws one
-    // If some day we want to see the errors thrown by pip too, use this condition instead:  (status != 0)
-    if (status < 0) {
-        FILE *fp = fdopen(logfd, "r");
-        if (!fp) {
-            remove(logfile);
-            return -1;
-        } else {
-            char line[BUFSIZ] = {0};
-            fflush(stdout);
-            fflush(stderr);
-            while (fgets(line, sizeof(line) - 1, fp) != NULL) {
-                fprintf(stderr, "%s", line);
-            }
-            fflush(stderr);
-            fclose(fp);
-        }
-    }
-    remove(logfile);
-    return proc.returncode == 0;
-}
-
-int conda_exec(const char *args) {
-    char command[PATH_MAX];
-    const char *mamba_commands[] = {
-            "build",
-            "install",
-            "update",
-            "create",
-            "list",
-            "search",
-            "run",
-            "info",
-            "clean",
-            "activate",
-            "deactivate",
-            NULL
-    };
-    char conda_as[6];
-    memset(conda_as, 0, sizeof(conda_as));
-
-    strcpy(conda_as, "conda");
-    for (size_t i = 0; mamba_commands[i] != NULL; i++) {
-        if (startswith(args, mamba_commands[i])) {
-            strcpy(conda_as, "mamba");
-            break;
-        }
-    }
-
-    snprintf(command, sizeof(command) - 1, "%s %s", conda_as, args);
-    msg(STASIS_MSG_L3, "Executing: %s\n", command);
-    return system(command);
-}
-
-int conda_activate(const char *root, const char *env_name) {
-    int fd = -1;
-    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};
-    char path_mamba[PATH_MAX] = {0};
-    char logfile[PATH_MAX] = {0};
-    struct Process proc;
-    memset(&proc, 0, sizeof(proc));
-
-    // Where to find conda's init scripts
-    sprintf(path_conda, "%s%s", root, init_script_conda);
-    sprintf(path_mamba, "%s%s", root, init_script_mamba);
-
-    // Set the path to our stdout log
-    // Emulate mktemp()'s behavior. Give us a unique file name, but don't use
-    // the file handle at all. We'll open it as a FILE stream soon enough.
-    sprintf(logfile, "%s/%s", globals.tmpdir, "shell_XXXXXX");
-    fd = mkstemp(logfile);
-    if (fd < 0) {
-       perror(logfile);
-       return -1;
-    }
-    close(fd);
-
-    // Configure our process for output to a log file
-    strcpy(proc.f_stdout, logfile);
-
-    // Verify conda's init scripts are available
-    if (access(path_conda, F_OK) < 0) {
-        perror(path_conda);
-        remove(logfile);
-        return -1;
-    }
-
-    if (access(path_mamba, F_OK) < 0) {
-        perror(path_mamba);
-        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);
-    int retval = shell(&proc, command);
-    if (retval) {
-        // it didn't work; drop out for cleanup
-        remove(logfile);
-        return retval;
-    }
-
-    // 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);
-        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;
-}
-
-int conda_check_required() {
-    int status = 0;
-    struct StrList *result = NULL;
-    char cmd[PATH_MAX] = {0};
-    const char *conda_minimum_viable_tools[] = {
-            "boa",
-            "conda-build",
-            "conda-verify",
-            NULL
-    };
-
-    // Construct a "conda list" command that searches for all required packages
-    // using conda's (python's) regex matching
-    strcat(cmd, "conda list '");
-    for (size_t i = 0; conda_minimum_viable_tools[i] != NULL; i++) {
-        strcat(cmd, "^");
-        strcat(cmd, conda_minimum_viable_tools[i]);
-        if (conda_minimum_viable_tools[i + 1] != NULL) {
-            strcat(cmd, "|");
-        }
-    }
-    strcat(cmd, "' | cut -d ' ' -f 1");
-
-    // Verify all required packages are installed
-    char *cmd_out = shell_output(cmd, &status);
-    if (cmd_out) {
-        size_t found = 0;
-        result = strlist_init();
-        strlist_append_tokenize(result, cmd_out, "\n");
-        for (size_t i = 0; i < strlist_count(result); i++) {
-            char *item = strlist_item(result, i);
-            if (isempty(item) || startswith(item, "#")) {
-                continue;
-            }
-
-            for (size_t x = 0; conda_minimum_viable_tools[x] != NULL; x++) {
-                if (!strcmp(item, conda_minimum_viable_tools[x])) {
-                    found++;
-                }
-            }
-        }
-        if (found < (sizeof(conda_minimum_viable_tools) / sizeof(*conda_minimum_viable_tools)) - 1) {
-            guard_free(cmd_out);
-            guard_strlist_free(&result);
-            return 1;
-        }
-        guard_free(cmd_out);
-        guard_strlist_free(&result);
-    } else {
-        msg(STASIS_MSG_ERROR | STASIS_MSG_L2, "The base package requirement check could not be performed\n");
-        return 2;
-    }
-    return 0;
-}
-
-int conda_setup_headless() {
-    if (globals.verbose) {
-        conda_exec("config --system --set quiet false");
-    } else {
-        // Not verbose, so squelch conda's noise
-        conda_exec("config --system --set quiet true");
-    }
-
-    // Configure conda for headless CI
-    conda_exec("config --system --set auto_update_conda false");     // never update conda automatically
-    conda_exec("config --system --set notify_outdated_conda false"); // never notify about outdated conda version
-    conda_exec("config --system --set always_yes true");             // never prompt for input
-    conda_exec("config --system --set safety_checks disabled");      // speedup
-    conda_exec("config --system --set rollback_enabled false");      // speedup
-    conda_exec("config --system --set report_errors false");         // disable data sharing
-    conda_exec("config --system --set solver libmamba");             // use a real solver
-
-    char cmd[PATH_MAX];
-    size_t total = 0;
-    if (globals.conda_packages && strlist_count(globals.conda_packages)) {
-        memset(cmd, 0, sizeof(cmd));
-        strcpy(cmd, "install ");
-
-        total = strlist_count(globals.conda_packages);
-        for (size_t i = 0; i < total; i++) {
-            char *item = strlist_item(globals.conda_packages, i);
-            if (isempty(item)) {
-                continue;
-            }
-            sprintf(cmd + strlen(cmd), "'%s'", item);
-            if (i < total - 1) {
-                strcat(cmd, " ");
-            }
-        }
-
-        if (conda_exec(cmd)) {
-            msg(STASIS_MSG_ERROR | STASIS_MSG_L2, "Unable to install user-defined base packages (conda)\n");
-            return 1;
-        }
-    }
-
-    if (globals.pip_packages && strlist_count(globals.pip_packages)) {
-        memset(cmd, 0, sizeof(cmd));
-        strcpy(cmd, "install ");
-
-        total = strlist_count(globals.pip_packages);
-        for (size_t i = 0; i < total; i++) {
-            char *item = strlist_item(globals.pip_packages, i);
-            if (isempty(item)) {
-                continue;
-            }
-            sprintf(cmd + strlen(cmd), "'%s'", item);
-            if (i < total - 1) {
-                strcat(cmd, " ");
-            }
-        }
-
-        if (pip_exec(cmd)) {
-            msg(STASIS_MSG_ERROR | STASIS_MSG_L2, "Unable to install user-defined base packages (pip)\n");
-            return 1;
-        }
-    }
-
-    if (conda_check_required()) {
-        msg(STASIS_MSG_ERROR | STASIS_MSG_L2, "Your STASIS configuration lacks the bare"
-                                                  " minimum software required to build conda packages."
-                                                  " Please fix it.\n");
-        return 1;
-    }
-
-    if (globals.always_update_base_environment) {
-        if (conda_exec("update --all")) {
-            fprintf(stderr, "conda update was unsuccessful\n");
-            return 1;
-        }
-    }
-
-    return 0;
-}
-
-int conda_env_create_from_uri(char *name, char *uri) {
-    char env_command[PATH_MAX];
-    sprintf(env_command, "env create -n %s -f %s", name, uri);
-    return conda_exec(env_command);
-}
-
-int conda_env_create(char *name, char *python_version, char *packages) {
-    char env_command[PATH_MAX];
-    sprintf(env_command, "create -n %s python=%s %s", name, python_version, packages ? packages : "");
-    return conda_exec(env_command);
-}
-
-int conda_env_remove(char *name) {
-    char env_command[PATH_MAX];
-    sprintf(env_command, "env remove -n %s", name);
-    return conda_exec(env_command);
-}
-
-int conda_env_export(char *name, char *output_dir, char *output_filename) {
-    char env_command[PATH_MAX];
-    sprintf(env_command, "env export -n %s -f %s/%s.yml", name, output_dir, output_filename);
-    return conda_exec(env_command);
-}
-
-char *conda_get_active_environment() {
-    const char *name = getenv("CONDA_DEFAULT_ENV");
-    if (!name) {
-        return NULL;
-    }
-
-    char *result = NULL;
-    result = strdup(name);
-    if (!result) {
-        return NULL;
-    }
-
-    return result;
-}
-
-int conda_provides(const char *spec) {
-    struct Process proc;
-    memset(&proc, 0, sizeof(proc));
-    strcpy(proc.f_stdout, "/dev/null");
-    strcpy(proc.f_stderr, "/dev/null");
-
-    // It's worth noting the departure from using conda_exec() here:
-    // conda_exec() expects the program output to be visible to the user.
-    // For this operation we only need the exit value.
-    char cmd[PATH_MAX] = {0};
-    snprintf(cmd, sizeof(cmd) - 1, "mamba search --use-index-cache %s", spec);
-    if (shell(&proc, cmd) < 0) {
-        fprintf(stderr, "shell: %s", strerror(errno));
-        return -1;
-    }
-    return proc.returncode == 0;
-}
-
-int conda_index(const char *path) {
-    char command[PATH_MAX];
-    sprintf(command, "index %s", path);
-    return conda_exec(command);
-}