Added extra api reference stuff

.github/workflows/docs.yml

@@ -61,7 +61,9 @@ jobs:
           pip install -e .
 
       - name: Generate API Reference
-        run: python docs/api.py
+        run: |
+          python docs/api.py
+          quartodoc interlinks docs/_quarto.yml
 
       - name: Generate docs
         run: |

docs/.gitignore

@@ -1,6 +1,7 @@
 /.quarto/
-/_site/
 /_freeze/
+/_inv/
+/_site/
 /api/*
 !api/.gitkeep
 *.jupyter_cache/

docs/_extensions/machow/interlinks/.gitignore

@@ -0,0 +1,3 @@
+*.html
+*.pdf
+*_files/

docs/_extensions/machow/interlinks/_extension.yml

@@ -0,0 +1,7 @@
+title: Interlinks
+author: Michael Chow
+version: 1.1.0
+quarto-required: ">=1.2.0"
+contributes:
+  filters:
+    - interlinks.lua

docs/_extensions/machow/interlinks/interlinks.lua

@@ -0,0 +1,254 @@
+local function read_inv_text(filename)
+    -- read file
+    local file = io.open(filename, "r")
+    if file == nil then
+        return nil
+    end
+    local str = file:read("a")
+    file:close()
+
+
+    local project = str:match("# Project: (%S+)")
+    local version = str:match("# Version: (%S+)")
+
+    local data = {project = project, version = version, items = {}}
+
+    local ptn_data =
+        "^" ..
+        "(.-)%s+" ..        -- name
+        "([%S:]-):" ..      -- domain
+        "([%S]+)%s+" ..     -- role
+        "(%-?%d+)%s+" ..     -- priority
+        "(%S*)%s+" ..       -- uri
+        "(.-)\r?$"         -- dispname
+
+
+    -- Iterate through each line in the file content
+    for line in str:gmatch("[^\r\n]+") do
+        if not line:match("^#") then
+            -- Match each line against the pattern
+            local name, domain, role, priority, uri, dispName = line:match(ptn_data)
+
+            -- if name is nil, raise an error
+            if name == nil then
+                error("Error parsing line: " .. line)
+            end
+
+            data.items[#data.items + 1] = {
+                name = name,
+                domain = domain,
+                role = role,
+                priority = priority,
+                uri = uri,
+                dispName = dispName
+            }
+        end
+    end
+    return data
+end
+
+local function read_json(filename)
+
+    local file = io.open(filename, "r")
+    if file == nil then
+        return nil
+    end
+    local str = file:read("a")
+    file:close()
+
+    local decoded = quarto.json.decode(str)
+    return decoded
+end
+
+local function read_inv_text_or_json(base_name)
+    local file = io.open(base_name .. ".txt", "r")
+    if file then
+        -- TODO: refactors so we don't just close the file immediately
+        io.close(file)
+        json = read_inv_text(base_name .. ".txt")
+
+    else
+        json = read_json(base_name .. ".json")
+    end
+
+    return json
+end
+
+local inventory = {}
+
+local function lookup(search_object)
+
+    local results = {}
+    for _, inv in ipairs(inventory) do
+        for _, item in ipairs(inv.items) do
+            -- e.g. :external+<inv_name>:<domain>:<role>:`<name>`
+            if item.inv_name and item.inv_name ~= search_object.inv_name then
+                goto continue
+            end
+
+            if item.name ~= search_object.name then
+                goto continue
+            end
+
+            if search_object.role and item.role ~= search_object.role then
+                goto continue
+            end
+
+            if search_object.domain and item.domain ~= search_object.domain then
+                goto continue
+            else
+                if search_object.domain or item.domain == "py" then
+                  table.insert(results, item)
+                end
+
+                goto continue
+            end
+
+            ::continue::
+        end
+    end
+
+    if #results == 1 then
+        return results[1]
+    end
+    if #results > 1 then
+        quarto.log.warning("Found multiple matches for " .. search_object.name .. ", using the first match.")
+        return results[1]
+    end
+    if #results == 0 then
+        quarto.log.warning("Found no matches for object:\n", search_object)
+    end
+
+    return nil
+end
+
+local function mysplit (inputstr, sep)
+    if sep == nil then
+            sep = "%s"
+    end
+    local t={}
+    for str in string.gmatch(inputstr, "([^"..sep.."]+)") do
+            table.insert(t, str)
+    end
+    return t
+end
+
+local function normalize_role(role)
+    if role == "func" then
+        return "function"
+    end
+    return role
+end
+
+local function build_search_object(str)
+    local starts_with_colon = str:sub(1, 1) == ":"
+    local search = {}
+    if starts_with_colon then
+        local t = mysplit(str, ":")
+        if #t == 2 then
+            -- e.g. :py:func:`my_func`
+            search.role = normalize_role(t[1])
+            search.name = t[2]:match("%%60(.*)%%60")
+        elseif #t == 3 then
+            -- e.g. :py:func:`my_func`
+            search.domain = t[1]
+            search.role = normalize_role(t[2])
+            search.name = t[3]:match("%%60(.*)%%60")
+        elseif #t == 4 then
+            -- e.g. :ext+inv:py:func:`my_func`
+            search.external = true
+
+            search.inv_name = t[1]:match("external%+(.*)")
+            search.domain = t[2]
+            search.role = normalize_role(t[3])
+            search.name = t[4]:match("%%60(.*)%%60")
+        else
+            quarto.log.warning("couldn't parse this link: " .. str)
+            return {}
+        end
+    else
+        search.name = str:match("%%60(.*)%%60")
+    end
+
+    if search.name == nil then
+        quarto.log.warning("couldn't parse this link: " .. str)
+        return {}
+    end
+
+    if search.name:sub(1, 1) == "~" then
+        search.shortened = true
+        search.name = search.name:sub(2, -1)
+    end
+    return search
+end
+
+local function report_broken_link(link, search_object, replacement)
+    -- TODO: how to unescape html elements like [?
+    return pandoc.Code(pandoc.utils.stringify(link.content))
+end
+
+function Link(link)
+    -- do not process regular links ----
+    if not link.target:match("%%60") then
+        return link
+    end
+
+    -- lookup item ----
+    local search = build_search_object(link.target)
+    local item = lookup(search)
+
+    -- determine replacement, used if no link text specified ----
+    local original_text = pandoc.utils.stringify(link.content)
+    local replacement = search.name
+    if search.shortened then
+        local t = mysplit(search.name, ".")
+        replacement = t[#t]
+    end
+
+    -- set link text ----
+    if original_text == "" and replacement ~= nil then
+        link.content = pandoc.Code(replacement)
+    end
+
+    -- report broken links ----
+    if item == nil then
+        return report_broken_link(link, search)
+    end
+    link.target = item.uri:gsub("%$$", search.name)
+
+
+    return link
+end
+
+local function fixup_json(json, prefix)
+    for _, item in ipairs(json.items) do
+        item.uri = prefix .. item.uri
+    end
+    table.insert(inventory, json)
+end
+
+return {
+    {
+        Meta = function(meta)
+            local json
+            local prefix
+            if meta.interlinks and meta.interlinks.sources then
+                for k, v in pairs(meta.interlinks.sources) do
+                    local base_name = quarto.project.offset .. "/_inv/" .. k .. "_objects"
+                    json = read_inv_text_or_json(base_name)
+                    prefix = pandoc.utils.stringify(v.url)
+                    if json ~= nil then
+                        fixup_json(json, prefix)
+                    end
+                end
+            end
+            json = read_inv_text_or_json(quarto.project.offset .. "/objects")
+            if json ~= nil then
+                fixup_json(json, "/")
+            end
+        end
+    },
+    {
+        Link = Link
+    }
+}

docs/_quarto.yml

@@ -6,6 +6,23 @@ project:
     - "*.ipynb"
     - "!PDF_Documentation.qmd"
 
+filters:
+   - include-code-files
+   - interlinks
+  #  - section-bibliographies
+
+interlinks:
+  sources:
+    python:
+      url: https://docs.python.org/3/
+    numpy:
+      url: https://numpy.org/doc/stable/
+
+metadata-files:
+  - api/_sidebar.yml
+
+number-sections: false
+
 website:
   title: "Delft FIAT"
   favicon: _static/logo.png
@@ -87,25 +104,17 @@ format:
 # bibliography: references.bib
 # citeproc: false
 
-number-sections: false
-
-filters:
-   - include-code-files
-  #  - section-bibliographies
-
 execute:
   freeze: auto
   cache: true
 
-metadata-files:
-  - api/_sidebar.yml
-
 quartodoc:
   parser: numpy
   package: fiat
   title: API Reference
   style: pkgdown
   dir: api
+  render_interlinks: true
   sidebar: api/_sidebar.yml
   options:
     include_imports: true
@@ -114,7 +123,6 @@ quartodoc:
   # Basics of FIAT
   sections:
     - title: Basics
-      desc: The higher level components of FIAT.
     - subtitle: Core
       desc: Two main components of working with FIAT.
       package: fiat
@@ -134,7 +142,6 @@ quartodoc:
 
     # Geospatial methods
     - title: GIS
-      desc: Geospatial bound operations.
     - subtitle: Geometry (vector)
       desc: Geometry specific methods
       package: fiat.gis.geom
@@ -162,16 +169,15 @@ quartodoc:
 
     # I/O module
     - title: I/O
-      desc: Input/ output bound operations.
     - subtitle: Methods
-      desc: Input/ output methods
+      desc: Input/ output bound operations
       package: fiat.io
       contents:
         - open_csv
         - open_geom
         - open_grid
     - subtitle: Objects
-      desc:
+      desc: Objects constructed from data
       package: fiat.io
       contents:
         - name: GeomSource

pyproject.toml

@@ -163,7 +163,7 @@ line-length = 88
 # enable pydocstyle (E), pyflake (F) and isort (I), pytest-style (PT)
 select = ["E", "F", "I", "PT", "D"]
 ignore-init-module-imports = true
-ignore = ["D211", "D213", "E741", "D105", "E712", "B904"]
+ignore = ["B904", "D105", "D211", "D213", "D301", "E712", "E741"]
 exclude = ["docs"]
 
 [tool.ruff.per-file-ignores]

src/fiat/cfg.py

@@ -1,6 +1,7 @@
 """The config interpreter of FIAT."""
 
 import os
+from pathlib import Path
 from typing import Any
 
 import tomli
@@ -12,7 +13,6 @@
     check_config_grid,
 )
 from fiat.util import (
-    Path,
     create_hidden_folder,
     flatten_dict,
     generic_folder_check,