add mkdocs gh action; clean up docs

.github/workflows/build.yml

@@ -1,6 +1,6 @@
 # Builds and runs pytest on ubuntu-latest
 # Tests python versions >=3.6
-name: Build
+name: build
 
 on:
   push:

.github/workflows/documentation.yml

@@ -0,0 +1,17 @@
+name: deploy documentation
+on:
+  push:
+    branches:
+      - main
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.x
+      - run: pip install mkdocs
+      - run: mkdocs gh-deploy --force
+env:
+  GH_TOKEN: ${{ secrets.GH_TOKEN }}

docs/CNAME

@@ -0,0 +1 @@
+koza.monarchinitiative.org

docs/ingest_configuration.md

@@ -41,11 +41,15 @@ delimiter: '\t'
 # Optional delimiter for header row
 header_delimiter: '|' 
 
-# Boolean to configure presence of header, default is true
-has_header: 'False'
-
-# Number of lines to be ignored at the head of an ingest data file, default is 0
-skip_lines: 10 
+# Optional, int | 'infer' | 'none', Default = 'infer'
+# The index (0 based) in which the header appears in the file.
+#
+# If header is set to 'infer' the headers will be set to the first
+# line that is not blank or commented with a hash.
+#
+# If header is set to 'none' then the columns field will be used,
+# or raise a ValueError if columns are not supplied
+header: 0
 
 # Boolean to skip blank lines, default is true
 skip_blank_lines: True

koza/io/reader/csv_reader.py

@@ -61,7 +61,9 @@ def __init__(
         :param header: 0 based index of the file that contains the header,
                        or header mode 'infer'|'none' ( default='infer' )
                        if 'infer' will use the first non-empty and uncommented line
-                       if 'none' will use the field_type_map keys, if field_type_map
+                       if 'none' will use the user supplied columns in field_type_map keys,
+                           if field_type_map is None this will raise a ValueError
+
         :param header_delimiter: delimiter for the header row, default = self.delimiter
         :param dialect: csv dialect, default=excel
         :param skip_blank_lines: true to skip blank lines, false to insert NaN for blank lines,

koza/model/config/source_config.py

@@ -160,7 +160,8 @@ class SourceConfig:
             header appears in the file.  If header is set to infer
             the headers will be set to the first line that is not blank
             or commented with a hash.  If header is set to 'none'
-            then the columns field will be used
+            then the columns field will be used, or raise a ValueError
+            if columns are not supplied
 
     delimiter:
     separator string similar to what works in str.split()
@@ -256,6 +257,14 @@ def __post_init_post_parse__(self):
                 for column in self.columns
             ]
 
+        if self.header == HeaderMode.none and not self.columns:
+            raise ValueError(
+                    f"there is no header and columns have not been supplied\n"
+                    f"configure the 'columns' field or set header to the 0-based"
+                     "index in which it appears in the file, or set this value to"
+                    "'infer'"
+            )
+
         for column in filtered_columns:
             if column not in all_columns:
                 raise (ValueError(f"Filter column {column} not in column list"))