add: CLI improvements and small documentation updates

Things done:
    * config path should search config file in the following order: cli
      option, environment, xdg_path
    * Implement a retrain command.
    * when you require more keys than the ones available in the input,
      stop the program.

3 files changed, 25 insertions, 9 deletions

diff --git a/src/main.c b/src/main.c
index 38f26ad..22737dc 100644
--- a/src/main.c
+++ b/src/main.c
@@ -51,7 +51,7 @@ void load_config(struct Configs *cfg, int n_args, ...)
         } else break;
     }
     va_end(ap);
-    die("load_config() Error:");
+    die("load_config('%s') Error:", filepath);
 }
 
 Layer * load_network(struct Configs cfg)
@@ -88,11 +88,11 @@ struct Cost load_loss(struct Configs cfg)
 }
 
 int main(int argc, char *argv[]) {
-    char default_config_path[512];
+    char default_config_path[512], *env_config_path;
     struct Configs ml_configs = {
         .epochs = 100,
         .alpha = 1e-5,
-        .config_filepath = "utils/settings.cfg",
+        .config_filepath = "",
         .network_size = 0,
         .only_out = false,
         .decimal_precision = -1,
@@ -103,9 +103,15 @@ int main(int argc, char *argv[]) {
     // First past to check if --config option was put
     util_load_cli(&ml_configs, argc, argv);
     optind = 1;
+
     // Load configs with different possible paths
     sprintf(default_config_path, "%s/%s", getenv("HOME"), ".config/ml/ml.cfg");
-    load_config(&ml_configs, 2, ml_configs.config_filepath, default_config_path);
+    env_config_path = (getenv("ML_CONFIG_PATH"))? getenv("ML_CONFIG_PATH"):"";
+
+    load_config(&ml_configs, 3,
+                ml_configs.config_filepath,
+                env_config_path,
+                default_config_path);
 
     // re-read cli options again, to overwrite file configuration options
     util_load_cli(&ml_configs, argc, argv);
@@ -115,12 +121,17 @@ int main(int argc, char *argv[]) {
     Layer *network = load_network(ml_configs);
 
     Array X, y;
-    if (!strcmp("train", argv[0])) {
+    if (!strcmp("train", argv[0]) || !strcmp("retrain", argv[0])) {
         file_read(argv[1], &X, &y,
                   ml_configs.input_keys, ml_configs.n_input_keys,
                   ml_configs.label_keys, ml_configs.n_label_keys,
                   true, ml_configs.file_format);
-        nn_network_init_weights(network, ml_configs.network_size, X.shape[1], true);
+        if (!strcmp("train", argv[0])) {
+            nn_network_init_weights(network, ml_configs.network_size, X.shape[1], true);
+        } else if (!strcmp("retrain", argv[0])) {
+            nn_network_init_weights(network, ml_configs.network_size, X.shape[1], false);
+            nn_network_read_weights(ml_configs.weights_filepath, network, ml_configs.network_size);
+        }
         nn_network_train(
                 network, ml_configs.network_size,
                 X.data, X.shape,
@@ -139,7 +150,7 @@ int main(int argc, char *argv[]) {
         nn_network_read_weights(ml_configs.weights_filepath, network, ml_configs.network_size);
         nn_network_predict(y.data, y.shape, X.data, X.shape, network, ml_configs.network_size);
 
-        // If neither output and file_format defined use input to define the format
+        // If neither output and file_format defined use input to define the output format
         if (!ml_configs.file_format && !ml_configs.out_filepath) {
             ml_configs.file_format = file_format_infer(ml_configs.in_filepath);
         }
diff --git a/src/parse.c b/src/parse.c
index cea595b..a06f0f3 100644
--- a/src/parse.c
+++ b/src/parse.c
@@ -187,6 +187,11 @@ void json_read(
             die("json_read() Error: unexpected JSON data received, expecting an object");
         }
 
+        if ((size_t)json_object_object_length(item) < n_input_keys + n_out_keys) {
+            die("json_read() Error: the number of keys required is greater "
+                "than the keys available in the object:\n%s",
+                json_object_to_json_string_ext(item, JSON_C_TO_STRING_PRETTY));
+        }
         for (j = 0; j < n_input_keys; j++) {
             value = json_object_object_get(item, in_keys[j]);
             obj_type = json_object_get_type(value);
@@ -517,7 +522,7 @@ int main(int argc, char *argv[]) {
 
     // use input format if format variable is not defined
     format = (!format && !strcmp(out_file, "-")) ? file_format_infer(in_file) : format;
-    file_write(out_file, X, y, in_cols, n_in_cols, out_cols, n_out_cols, true, format);
+    file_write(out_file, X, y, in_cols, n_in_cols, out_cols, n_out_cols, true, format, -1);
     for (i = 0; i < n_in_cols; i++) free(in_cols[i]);
     for (i = 0; i < n_out_cols; i++) free(out_cols[i]);
 
diff --git a/src/util.c b/src/util.c
index 4621836..9a00aa3 100644
--- a/src/util.c
+++ b/src/util.c
@@ -91,7 +91,7 @@ void usage(int exit_code)
 {
     FILE *fp = (!exit_code) ? stdout : stderr;
     fprintf(fp,
-            "Usage: ml train [Options] FILE\n"
+            "Usage: ml [re]train [Options] FILE\n"
             "   or: ml predict [-Ohv] [-f FORMAT] [-o FILE] [-p INT] FILE\n"
             "\n"
             "Options:\n"