increase logo size and clean api export(s)

marisco/inout.py

@@ -1,4 +1,4 @@
-"""Files reader and writer"""
+"""Files reader and writer."""
 
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/api/inout.ipynb.
 
@@ -11,12 +11,14 @@
 
 # %% ../nbs/api/inout.ipynb 3
 def write_toml(fname, cfg):
+    "Write a TOML file from a dictionary."
     print(f'Creating {fname}')
     with open(fname, "wb") as f:
         tomli_w.dump(cfg, f)
 
 # %% ../nbs/api/inout.ipynb 4
 def read_toml(fname):
+    "Read a TOML file into a dictionary."
     with open(fname, "rb") as f:
         config = tomli.load(f)
     return config

marisco/nc_template.py

@@ -35,7 +35,7 @@ def __init__(self,
         self.dim = cdl['dim']
         self.enum_types = {}
 
-# %% ../nbs/api/nc_template.ipynb 9
+# %% ../nbs/api/nc_template.ipynb 8
 @patch
 def nuclide_vars(
     self:NCTemplater,
@@ -66,7 +66,7 @@ def nuclide_vars(
         )
     ]
 
-# %% ../nbs/api/nc_template.ipynb 12
+# %% ../nbs/api/nc_template.ipynb 11
 @patch
 def derive(
     self:NCTemplater,
@@ -81,15 +81,15 @@ def derive(
         'attrs': {key: nuclide['attrs'][key] + suffix['attrs'][key] for key in nuclide['attrs']}
         }
 
-# %% ../nbs/api/nc_template.ipynb 18
+# %% ../nbs/api/nc_template.ipynb 17
 @patch
 def create_enum_types(self:NCTemplater):
     "Create enumeration types"
     for name, enum in self.enum_dicts.items(): 
         if self.verbose: print(f'Creating {name} enumeration type')
         self.enum_types[name] = self.nc.createEnumType(np.int_, name, enum)
 
-# %% ../nbs/api/nc_template.ipynb 19
+# %% ../nbs/api/nc_template.ipynb 18
 @patch
 def create_groups(self:NCTemplater):
     "Create NetCDF groups"
@@ -98,7 +98,7 @@ def create_groups(self:NCTemplater):
         grp = self.nc.createGroup(grp_name)
         self.create_variables(grp)
 
-# %% ../nbs/api/nc_template.ipynb 20
+# %% ../nbs/api/nc_template.ipynb 19
 @patch
 def create_variables(self:NCTemplater, 
                      grp:netCDF4.Group, # NetCDF group
@@ -109,7 +109,7 @@ def create_variables(self:NCTemplater,
         self.create_group_specific_variables(grp)
         self.create_analyte_variables(grp)
 
-# %% ../nbs/api/nc_template.ipynb 21
+# %% ../nbs/api/nc_template.ipynb 20
 @patch
 def create_default_variables(self:NCTemplater, 
                              grp:netCDF4.Group, # NetCDF group
@@ -118,7 +118,7 @@ def create_default_variables(self:NCTemplater,
         vars = self.cdl['vars']['defaults'].values()
         for var in vars: self.create_variable(grp, var)
 
-# %% ../nbs/api/nc_template.ipynb 22
+# %% ../nbs/api/nc_template.ipynb 21
 @patch
 def create_group_specific_variables(self:NCTemplater, 
                              grp:netCDF4.Group, # NetCDF group
@@ -128,7 +128,7 @@ def create_group_specific_variables(self:NCTemplater,
         for var in vars.get(name2grp(grp.name, self.cdl), {}).values(): 
             self.create_variable(grp, var)
 
-# %% ../nbs/api/nc_template.ipynb 23
+# %% ../nbs/api/nc_template.ipynb 22
 @patch
 def create_analyte_variables(self:NCTemplater, 
                              grp:netCDF4.Group, # NetCDF group
@@ -139,7 +139,7 @@ def create_analyte_variables(self:NCTemplater,
         for v in self.cdl['vars']['suffixes'].values(): 
             self.create_variable(grp, self.derive(var, v))
 
-# %% ../nbs/api/nc_template.ipynb 24
+# %% ../nbs/api/nc_template.ipynb 23
 @patch
 def create_variable(self:NCTemplater, 
                     grp:netCDF4.Group, # NetCDF group
@@ -152,7 +152,7 @@ def create_variable(self:NCTemplater,
                                 self.dim['name'])
     nc_var.setncatts(attrs) 
 
-# %% ../nbs/api/nc_template.ipynb 26
+# %% ../nbs/api/nc_template.ipynb 24
 @patch
 def generate(self:NCTemplater):
     "Generate CDL"

marisco/utils.py

@@ -42,6 +42,7 @@ def get_unique_across_dfs(dfs:dict,  # Dictionary of dataframes
 
 # %% ../nbs/api/utils.ipynb 12
 class Remapper():
+    "Remap a data provider lookup table to a MARIS lookup table using fuzzy matching."
     def __init__(self,
                  provider_lut_df:pd.DataFrame, # Data provider lookup table to be remapped
                  maris_lut_fn:callable, # Function that returns the MARIS lookup table path
@@ -51,7 +52,6 @@ def __init__(self,
                  provider_col_key, # Data provider lookup table column name for the key
                  fname_cache  # Cache file name
                  ):
-        "Remap a data provider lookup table to a MARIS lookup table using fuzzy matching."
         fc.store_attr()
         self.cache_file = cache_path() / fname_cache
         self.maris_lut = maris_lut_fn()
@@ -140,6 +140,7 @@ def has_valid_varname(
 def get_bbox(df,
              coord_cols=('lon', 'lat')
             ):
+    "Get the bounding box of a DataFrame."
     x, y = coord_cols        
     arr = [(row[x], row[y]) for _, row in df.iterrows()]
     return MultiPoint(arr).envelope
@@ -150,7 +151,7 @@ def download_files_in_folder(owner:str,
                              src_dir:str, 
                              dest_dir:str
                              ):
-    "Make a GET request to the GitHub API to get the contents of the folder"
+    "Make a GET request to the GitHub API to get the contents of the folder."
     url = f"https://api.github.com/repos/{owner}/{repo}/contents/{src_dir}"
     response = requests.get(url)
 
@@ -182,7 +183,7 @@ def download_file(owner, repo, src_dir, dest_dir, fname):
 def match_worms(
     name:str # Name of species to look up in WoRMS
     ):
-    "Lookup `name` in WoRMS (fuzzy match)"
+    "Lookup `name` in WoRMS (fuzzy match)."
     url = 'https://www.marinespecies.org/rest/AphiaRecordsByMatchNames'
     params = {
         'scientificnames[]': [name],
@@ -201,15 +202,16 @@ def match_worms(
     else:
         return -1
 
-# %% ../nbs/api/utils.ipynb 37
+# %% ../nbs/api/utils.ipynb 32
 @dataclass
 class Match:
+    "Match between a data provider name and a MARIS lookup table."
     matched_id: int
     matched_maris_name: str
     source_name: str
     match_score: int
 
-# %% ../nbs/api/utils.ipynb 38
+# %% ../nbs/api/utils.ipynb 33
 def match_maris_lut(
     lut_path: str, # Path to MARIS species authoritative species look-up table
     data_provider_name: str, # Name of data provider nomenclature item to look up 
@@ -226,15 +228,15 @@ def match_maris_lut(
     df = df.sort_values(by='score', ascending=True)[:nresults]
     return df[[maris_id, maris_name, 'score']]
 
-# %% ../nbs/api/utils.ipynb 45
+# %% ../nbs/api/utils.ipynb 40
 def get_bbox(df,
              coord_cols=('lon', 'lat')
             ):
     x, y = coord_cols        
     arr = [(row[x], row[y]) for _, row in df.iterrows()]
     return MultiPoint(arr).envelope
 
-# %% ../nbs/api/utils.ipynb 52
+# %% ../nbs/api/utils.ipynb 47
 def download_files_in_folder(owner:str, 
                              repo:str, 
                              src_dir:str, 
@@ -268,7 +270,7 @@ def download_file(owner, repo, src_dir, dest_dir, fname):
     else:
         print(f"Error: {response.status_code}")
 
-# %% ../nbs/api/utils.ipynb 54
+# %% ../nbs/api/utils.ipynb 49
 def match_worms(
     name:str # Name of species to look up in WoRMS
     ):
@@ -291,7 +293,7 @@ def match_worms(
     else:
         return -1
 
-# %% ../nbs/api/utils.ipynb 65
+# %% ../nbs/api/utils.ipynb 54
 def test_dfs(
     dfs1:dict, # First dictionary of DataFrames to compare 
     dfs2:dict # Second dictionary of DataFrames to compare

nbs/api/callbacks.ipynb

@@ -28,7 +28,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#| exports\n",
+    "#| export\n",
     "import copy\n",
     "import fastcore.all as fc\n",
     "from operator import attrgetter\n",

nbs/api/configs.ipynb

@@ -27,7 +27,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#| exports\n",
+    "#| export\n",
     "from pathlib import Path\n",
     "import os\n",
     "import re\n",

nbs/api/inout.ipynb

@@ -17,7 +17,7 @@
    "metadata": {},
    "source": [
     "# Input/Output\n",
-    "> Files reader and writer"
+    "> Files reader and writer."
    ]
   },
   {
@@ -39,8 +39,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#| export\n",
+    "#| exports\n",
     "def write_toml(fname, cfg):\n",
+    "    \"Write a TOML file from a dictionary.\"\n",
     "    print(f'Creating {fname}')\n",
     "    with open(fname, \"wb\") as f:\n",
     "        tomli_w.dump(cfg, f)"
@@ -53,8 +54,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#| export\n",
+    "#| exports\n",
     "def read_toml(fname):\n",
+    "    \"Read a TOML file into a dictionary.\"\n",
     "    with open(fname, \"rb\") as f:\n",
     "        config = tomli.load(f)\n",
     "    return config"

nbs/api/metadata.ipynb

@@ -27,7 +27,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#| exports\n",
+    "#| export\n",
     "import pandas as pd\n",
     "import fastcore.all as fc\n",
     "from cftime import num2date\n",