fix cdl config file not available

marisco/metadata.py

@@ -1,8 +1,7 @@
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/api/metadata.ipynb.
 
 # %% auto 0
-__all__ = ['GLOB_ATTRS_TPL', 'GlobAttrsFeeder', 'BboxCB', 'DepthRangeCB', 'TimeRangeCB', 'ZoteroCB', 'KeyValuePairCB',
-           'ZoteroItem']
+__all__ = ['GlobAttrsFeeder', 'BboxCB', 'DepthRangeCB', 'TimeRangeCB', 'ZoteroCB', 'KeyValuePairCB', 'ZoteroItem']
 
 # %% ../nbs/api/metadata.ipynb 2
 import pandas as pd
@@ -11,18 +10,16 @@
 
 from .utils import (read_toml, get_bbox, 
                            Callback, run_cbs)
-from .configs import BASE_PATH, get_cfgs
+from .configs import BASE_PATH, get_cfgs, CONFIGS_CDL
 
 from cftime import num2date
 from pyzotero import zotero
 import json
 
-# %% ../nbs/api/metadata.ipynb 3
-GLOB_ATTRS_TPL = read_toml(BASE_PATH / 'cdl.toml')['global_attrs']
-
 # %% ../nbs/api/metadata.ipynb 4
 class GlobAttrsFeeder:
-    def __init__(self, dfs, cbs=None, attrs=GLOB_ATTRS_TPL, logs=[]): fc.store_attr()
+    def __init__(self, dfs, cbs=None, attrs=CONFIGS_CDL['global_attrs'], logs=[]): 
+        fc.store_attr()
 
     def callback(self):
         run_cbs(self.cbs, self)

marisco/utils.py

@@ -76,7 +76,7 @@ def get_bbox(df,
         arr.append((row[x], row[y]))
     return MultiPoint(arr).envelope
 
-# %% ../nbs/api/utils.ipynb 22
+# %% ../nbs/api/utils.ipynb 20
 def download_files_in_folder(owner, repo, src_dir, dest_dir):
     # 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}"
@@ -106,7 +106,7 @@ def download_file(owner, repo, src_dir, dest_dir, fname):
     else:
         print(f"Error: {response.status_code}")
 
-# %% ../nbs/api/utils.ipynb 24
+# %% ../nbs/api/utils.ipynb 22
 def match_worms(
     name:str # Name of species to look up in WoRMS
     ):

nbs/api/metadata.ipynb

@@ -34,7 +34,7 @@
     "\n",
     "from marisco.utils import (read_toml, get_bbox, \n",
     "                           Callback, run_cbs)\n",
-    "from marisco.configs import BASE_PATH, get_cfgs\n",
+    "from marisco.configs import BASE_PATH, get_cfgs, CONFIGS_CDL\n",
     "\n",
     "from cftime import num2date\n",
     "from pyzotero import zotero\n",
@@ -48,8 +48,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "#| export\n",
-    "GLOB_ATTRS_TPL = read_toml(BASE_PATH / 'cdl.toml')['global_attrs']"
+    "# GLOB_ATTRS_TPL = read_toml(BASE_PATH / 'cdl.toml')['global_attrs']"
    ]
   },
   {
@@ -61,7 +60,8 @@
    "source": [
     "#| export\n",
     "class GlobAttrsFeeder:\n",
-    "    def __init__(self, dfs, cbs=None, attrs=GLOB_ATTRS_TPL, logs=[]): fc.store_attr()\n",
+    "    def __init__(self, dfs, cbs=None, attrs=CONFIGS_CDL['global_attrs'], logs=[]): \n",
+    "        fc.store_attr()\n",
     "        \n",
     "    def callback(self):\n",
     "        run_cbs(self.cbs, self)\n",

nbs/api/utils.ipynb

@@ -277,33 +277,6 @@
     "bbox.wkt"
    ]
   },
-  {
-   "attachments": {},
-   "cell_type": "markdown",
-   "id": "7c2eef73",
-   "metadata": {},
-   "source": [
-    "## Notebooks"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b0a463a1",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "#| hide\n",
-    "# TO BE REMOVED: NOT USED ANYMORE - REFACTORED\n",
-    "def parametrize(notebook:str, # Notebook path\n",
-    "               ):\n",
-    "    \"Add `parameters` notebook cell tag when seeing `#| params` special character\"\n",
-    "    nb = nbformat.read(notebook, as_version=4)\n",
-    "    cell = [c for c in nb.cells if '#|params' in c.source.replace(' ', '')][0]\n",
-    "    cell.metadata = {'tags': ['parameters']}\n",
-    "    nbformat.write(nb, notebook)"
-   ]
-  },
   {
    "attachments": {},
    "cell_type": "markdown",