Update stdout and comments

Author: mikecormier

ggd/check_recipe.py

@@ -220,7 +220,7 @@ def _install(bz2, recipe_name, debug=False, meta_recipe=False, env_var_dir = "",
     5) env_var_dir:   (str)  The path to the meta-recipe tmp env var 
     6) env_var_file:  (str)  The file path to the meta-recipe tmp env var json file
     7) parent_name:   (str)  If a meta-recipe, the name of the parent meta-recipe
-    8) commands_file: (str)  THe path to the subseted commands used for the specific Meta-Recipe ID if meta-recipe 
+    8) commands_file: (str)  The path to the subsetted commands used for the specific Meta-Recipe ID if meta-recipe 
 
     Returns:
     +++++++
@@ -277,7 +277,7 @@ def _install(bz2, recipe_name, debug=False, meta_recipe=False, env_var_dir = "",
 
             ## Check for meta-recipe environment variables
             if op.exists(env_var_file):
-                print("\n:ggd:check-recipe: Loading Meta-Recipe ID specific environmnet variables")
+                print("\n:ggd:check-recipe: Loading Meta-Recipe ID specific environment variables")
 
                 ## Load environment variables from json file
                 meta_env_vars = json.load(open(env_var_file))
@@ -352,11 +352,11 @@ def get_recipe_from_bz2(fbz2):
 
     Parameters:
     ----------
-    1) fbz2: The file path to the pre-built bz2 ggd package
+    1) fbz2: (str) The file path to the pre-built bz2 ggd package
     
     Return:
     +++++++
-    1) The meta.yaml file as a dictionary 
+    1) (dict) The meta.yaml file as a dictionary 
     """
     import tarfile
 
@@ -393,8 +393,8 @@ def _check_build(species, build):
 
     Parameters:
     -----------
-    1) species: The supplied species for the recipe being built
-    2) build: The genome build for the recipe being built
+    1) species: (str) The supplied species for the recipe being built
+    2) build:   (str) The genome build for the recipe being built
 
     Returns:
     ++++++++
@@ -507,7 +507,7 @@ def check_recipe(parser, args):
         ## Create a tmp dir to store environment variables too. 
         env_var_tmp_dir, env_var_file_path, final_commands_files = create_tmp_meta_recipe_env_file()
 
-        ## Set meta-recipe specifc env vars
+        ## Set meta-recipe specific env vars
         os.environ["GGD_METARECIPE_ID"] = args.id
         os.environ["GGD_METARECIPE_ENV_VAR_FILE"] = env_var_file_path
         os.environ["GGD_METARECIPE_FINAL_COMMANDS_FILE"] = final_commands_files
@@ -559,7 +559,6 @@ def check_recipe(parser, args):
             shutil.rmtree(env_var_tmp_dir)
 
         ## Skip header check on meta recipe files
-        #if species != "meta-recipe" and build != "meta-recipe":
         ## Check that the file has a header
         if not check_header(install_path): 
             print("\n:ggd:check-recipe: !!ERROR!!")
@@ -640,7 +639,7 @@ def check_recipe(parser, args):
     else:  ## if already installed
         print("\n:ggd:check-recipe: Package already installed on your system")
         print(
-            '\nggd:check-recipe: If the "-du" flag (dont_uninstall) is NOT set this package will be uninstalled'
+            '\n:ggd:check-recipe: If the "-du" flag (dont_uninstall) is NOT set this package will be uninstalled'
         )
         print("\n:ggd:check-recipe: To recheck this recipe")
         if args.dont_uninstall == True:
@@ -723,14 +722,14 @@ def add_to_checksum_md5sums(installed_dir_path, yaml_file, recipe_checksum_file_
 
     Parameters:
     -----------
-    1) installed_dir_path: The directory path to the installed data files, excluding the version number
-    2) yaml_file: The meta.yaml file for the recipe
-    3) recipe_checksum_file_path: The file path to the checksum recipe to update
+    1) installed_dir_path:        (str) The directory path to the installed data files, excluding the version number
+    2) yaml_file:                 (str) The meta.yaml file for the recipe
+    3) recipe_checksum_file_path: (str) The file path to the checksum recipe to update
 
     Returns:
     ++++++++
     1) Nothing is returned. The checksum file is updated with each data file and it's md5sum.
-        Each data file will be placed on its own line with a tab seperating the file's md5sum.
+        Each data file will be placed on its own line with a tab separating the file's md5sum.
     """
     print(":ggd:check-recipe: Updating md5sums for final data files\n")
     import glob
@@ -740,7 +739,7 @@ def add_to_checksum_md5sums(installed_dir_path, yaml_file, recipe_checksum_file_
     with open(recipe_checksum_file_path, "w") as cs_file:
         installed_files = glob.glob(op.join(installed_dir_path, "*"))
 
-        ## Check the number of files are the same between the yaml file and the acutal data files
+        ## Check the number of files are the same between the yaml file and the actual data files
         final_files = yaml_file["about"]["tags"]["final-files"]
         assert len(final_files) == len(installed_files), (
             ":ggd:check-recipe: The number of installed files does not match the number of final files listed in the recipe."
@@ -763,7 +762,7 @@ def add_final_files(installed_dir_path, yaml_dict, recipe_path, extra_files):
     Method to iterate through and add each of the final data files from the processed data package to 
      the meta.yaml file of the checked recipe. (This should be called after the "check_files" function
      has passed.) 
-    The file types will be added as well. If they are common genomic file types, otherwise the 
+    The file types will be added as well. If they are common genomics file types, otherwise the 
      file extension will be used.
     The meta.yaml file will be re-written with the new file types and final files. 
     New meta.yaml fields = 
@@ -773,10 +772,10 @@ def add_final_files(installed_dir_path, yaml_dict, recipe_path, extra_files):
 
     Parameters:
     -----------
-    1) installed_dir_path: The directory path to the installed data files
-    2) yaml_dict: A dictionary of the meta.yaml file for the recipe
-    3) recipe_path: The directory path to the recipe being checked 
-    4) extra_files: The name of the extra files found from check_files method
+    1) installed_dir_path: (str)  The directory path to the installed data files
+    2) yaml_dict:          (dict) A dictionary of the meta.yaml file for the recipe
+    3) recipe_path:        (str)  The directory path to the recipe being checked 
+    4) extra_files:        (list) The name of the extra files found from check_files method
 
     Returns: 
     ++++++++
@@ -903,8 +902,8 @@ def check_final_files(installed_dir_path, yaml_file):
 
     Parameters:
     -----------
-    1) installed_dir_path: The directory path to the installed files
-    2) yaml_file: The meta.yaml file for the recipe
+    1) installed_dir_path: (str) The directory path to the installed files
+    2) yaml_file:          (str) The meta.yaml file for the recipe
 
     Returns:
     ++++++++
@@ -991,8 +990,8 @@ def remove_package_after_install(bz2, recipe_name, exit_num):
     
     Parameters:
     -----------
-    1) bz2: The bz2 file created during the conda build process of the data package
-    2) exit_num: The exit number to exit the program with
+    1) bz2:      (str) The bz2 file created during the conda build process of the data package
+    2) exit_num: (int) The exit number to exit the program with
     """
     from .utils import get_conda_package_list, update_installed_pkg_metadata
 
@@ -1037,7 +1036,7 @@ def remove_package_after_install(bz2, recipe_name, exit_num):
 
 
 def check_header(install_path):
-    """Method to check the final genomic headers have a header or not
+    """Method to check the final genomics headers have a header or not
 
     check_header
     ============
@@ -1054,11 +1053,11 @@ def check_header(install_path):
 
     Parameters:
     -----------
-    1) install_path: The path to the directory where the files have been installed into.
+    1) install_path: (str) The path to the directory where the files have been installed into.
 
     Returns:
     +++++++
-    True or False. 
+    (bool) True or False. 
      - True if a header exist or if only a warning was given
      - False if a header does not exists and is required
 
@@ -1282,7 +1281,7 @@ def check_files(
     before_files,
     bz2,
 ):
-    """Method to check the presence of correct genomic files """
+    """Method to check the presence of correct genomics files """
     from fnmatch import fnmatch
 
     P = "{species}/{build}:{recipe_name}".format(**locals())
@@ -1304,7 +1303,7 @@ def check_files(
 
     base_tbx_tbi = [
         x[:-3] for x in tbxs if x[:-3] in nons
-    ]  # Name of files that are bgzip and tabix3d
+    ]  # Name of files that are bgzip and tabixed
 
     nons = [x for x in nons if x not in tbxs]  # files not tabixed or tbi
     nons = [x for x in nons if x not in base_tbx_tbi]  # files not tabixed or tbi

ggd/install.py

@@ -55,7 +55,7 @@ def add_install(p):
         "--id",
         metavar="Meta-recipe ID",
         help = ("The ID to use for the meta recipe being installed. For example, if installing the GEO meta-recipe for GEO Accession ID GSE123, use `--id GSE123`"
-                " NOTE: GGD will NOT try to correcet the ID. The ID must be accurately entered with case sensitive alphanumeric order") 
+                " NOTE: GGD will NOT try to correct the ID. The ID must be accurately entered with case sensitive alphanumeric order") 
     )
 
     c.set_defaults(func=install)
@@ -129,7 +129,8 @@ def check_if_installed(ggd_recipe, ggd_jdict, prefix=None):
     2) ggd_jdict:  (dict) The channel specific metadata file as a dictionary 
     3) prefix:     (str)  The prefix/conda environment to check in
     
-    Retruns:
+    Returns:
+    ++++++++
     1) False if not installed
     2) True if it is installed
     """
@@ -161,7 +162,7 @@ def check_conda_installation(ggd_recipe, prefix=None):
     ========================
     This method is used to check if the ggd data package has been installed by the conda system,
      without being installed by the ggd system. If it has, the recipe needs to be uninstalled and 
-     reinstalled. If not, the system continues to install the package using ggd.
+     re-installed. If not, the system continues to install the package using ggd.
 
     Parameters:
     -----------
@@ -209,15 +210,15 @@ def get_idname_from_metarecipe(accession_id, meta_recipe_name, jdict):
     ===========================
     Get the new name based on an accession id for a recipe to be installed from a meta-recipe 
 
-    Paramters:
+    Parameters:
     ----------
     1) accession_id:     (str)  The meta-recipe id for the new name 
     2) meta_recipe_name: (str)  The name of the meta recipe which is used to install the new recipe
     3) jdict:            (dict) The channeldata metadata json file loaded as a dict. (Channel == the channel 
                                  the meta recipe is in)
     Returns:
     ++++++++
-    1) The id sepecific recipe name from the meta recipe
+    1) The id specific recipe name from the meta recipe
     """
 
     new_recipe_name = "{}-{}-v{}".format(accession_id, 
@@ -322,7 +323,7 @@ def install_from_cached(ggd_recipes, ggd_channel, ggd_jdict, debug=False, prefix
         prefix=target_prefix, remove_old=False, add_packages=ggd_recipes
     )
 
-    ## Checkusm
+    ## Checksum
     try:
         install_checksum(ggd_recipes, ggd_jdict, target_prefix)
     except ChecksumError as e:
@@ -438,7 +439,7 @@ def conda_install(ggd_recipes, ggd_channel, ggd_jdict, debug=False, prefix=None,
         try:
             import json
 
-            print("\n:ggd:install: Loading Meta-Recipe ID specific environmnet variables")
+            print("\n:ggd:install: Loading Meta-Recipe ID specific environment variables")
             ## Get the updated env var list
             meta_env_vars = json.load(open(env_var_file_path)) if os.path.exists(env_var_file_path) else {}
 
@@ -466,7 +467,7 @@ def conda_install(ggd_recipes, ggd_channel, ggd_jdict, debug=False, prefix=None,
                 fsize, tsize, bsize = get_file_size(os.path.join(path,f))
                 file_size_dict[f] = fsize
 
-            ## Update meta-recipe meatada 
+            ## Update meta-recipe metadata 
             success, new_bz2 = update_metarecipe_metadata(pkg_name = pkg_name,
                                                          env_var_dict = meta_env_vars,
                                                          parent_name = meta_recipe_name,
@@ -480,7 +481,7 @@ def conda_install(ggd_recipes, ggd_channel, ggd_jdict, debug=False, prefix=None,
         except Exception as e:
             from .uninstall import check_for_installation
             import traceback
-            print("\n:ggd:install: !!ERROR!! Post-Installation problems while updaing meta-recipe metadata")
+            print("\n:ggd:install: !!ERROR!! Post-Installation problems while updating meta-recipe metadata")
             print(str(e))
             print(traceback.print_exc())
             check_for_installation(
@@ -499,7 +500,7 @@ def conda_install(ggd_recipes, ggd_channel, ggd_jdict, debug=False, prefix=None,
         prefix=target_prefix, remove_old=False, add_packages=ggd_recipes, include_local = True if meta_recipe else False
     )
 
-    ## Checkusm
+    ## Checksum
     try:
         install_checksum(ggd_recipes, ggd_jdict, target_prefix, meta_recipe, meta_recipe_name)
     except ChecksumError as e:
@@ -662,8 +663,8 @@ def install_checksum(pkg_names, ggd_jdict, prefix=conda_root(), meta_recipe = Fa
 
         ## Get checksum dict
         if meta_recipe:
-            assert meta_recipe_name != "", "\n:ggd:install: !!ERROR!! Unable to preform checksum on a meta-recipe wihtout the parent meta-recipe name"
-            print("\n:ggd:install: NOTICE: Skipping checkusm for meta-recipe {} => {}".format(meta_recipe_name, ", ".join(pkg_names)))
+            assert meta_recipe_name != "", "\n:ggd:install: !!ERROR!! Unable to preform checksum on a meta-recipe without the parent meta-recipe name"
+            print("\n:ggd:install: NOTICE: Skipping checksum for meta-recipe {} => {}".format(meta_recipe_name, ", ".join(pkg_names)))
             checksum_dict = {}
 #            try:
 #                checksum_dict = get_meta_recipe_checksum(meta_recipe_name, pkg_name) 
@@ -702,12 +703,12 @@ def install_checksum(pkg_names, ggd_jdict, prefix=conda_root(), meta_recipe = Fa
 
 
 def copy_pkg_files_to_prefix(prefix, pkg_names, meta_recipe = False):
-    """Method to copy the tar and package files from the current conda envrionment to the target prefix
+    """Method to copy the tar and package files from the current conda environment to the target prefix
     
     copy_pkg_files_to_prefix
     ========================
-    This method is used to copy the tarball file and the pkg file from the current conda envrionment to the 
-     target prefix if the prefix flag is set. This will support pkg info lookup for data management when installing
+    This method is used to copy the tarball file and the pkg file from the current conda environment to the 
+     target prefix if the prefix flag is set. This will support pkg info lockup for data management when installing
      a package using the prefix flag
 
     Parameters:
@@ -828,7 +829,7 @@ def install(parser, args):
 
             ## Check number of packages
             if len(pkg_list) > 1:
-                print("\n:ggd:install: GGD is currenlty only able to install a single meta-recipe at a time. Please remove other pkgs and install them with a subsequent command")
+                print("\n:ggd:install: GGD is currently only able to install a single meta-recipe at a time. Please remove other pkgs and install them with a subsequent command")
                 sys.exit()
 
             ## Id must be lower case for conda
@@ -858,7 +859,7 @@ def install(parser, args):
 
             ## Check for success
             try:
-                assert (success), "\n:ggd:install: !!ERROR!! There was a problem updating the meta-recipe to the ID speciifc recipe"
+                assert (success), "\n:ggd:install: !!ERROR!! There was a problem updating the meta-recipe to the ID specific recipe"
             except AssertionError as e:
                 print(str(e))
                 if tmpdir:
@@ -881,7 +882,7 @@ def install(parser, args):
             from .check_recipe import _build
             try:
                 new_bz2 = _build(new_recipe_path, recipe_yaml, debug = True if args.debug else False)
-                assert (os.path.exists(new_bz2)), "\n:ggd:install: !!ERRORR!! There was a problem building the new recipe"
+                assert (os.path.exists(new_bz2)), "\n:ggd:install: !!ERROR!! There was a problem building the new recipe"
             except Exception as e:
                 print(str(e))
                 if tmpdir:

ggd/list_files.py

@@ -73,7 +73,7 @@ def in_ggd_channel(ggd_recipes, ggd_channel, C_ROOT, reporting=True, return_pkg_
     Method used to identify in the desired package is in the ggd-<channel>.
      If it is the the species, build, and version is returned. 
     
-     Mutliple ggd recipes can be checked, but if the return_pkg_list parameter is set to false only the 
+     Multiple ggd recipes can be checked, but if the return_pkg_list parameter is set to false only the 
       species, genome build, and version of the first ggd recipe are returned.  
      
     Parameters:
@@ -95,7 +95,7 @@ def in_ggd_channel(ggd_recipes, ggd_channel, C_ROOT, reporting=True, return_pkg_
       NOTE: Only the species, genome build, and version for the first recipe be returned.
     if return_pkg_list is True:
         1) the pkg list
-        2) the channel specific dicitionary of packages
+        2) the channel specific dictionary of packages
     """
 
     from .search import load_json, load_json_from_url, search_packages
@@ -138,7 +138,7 @@ def get_package_list(j_dict):
 
         Returns:
         ++++++++
-        1) (list) The pckages that were found
+        1) (list) The packages that were found
         """
 
         package_list = []