Allow plain text .qmd files as source notebooks

.gitignore

@@ -149,4 +149,3 @@ checklink/cookies.txt
 
 # .gitconfig is now autogenerated
 .gitconfig
-

index.ipynb

@@ -0,0 +1,140 @@
+{
+ "cells": [
+  {
+   "cell_type": "raw",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "output-file: index.html\n",
+    "title: HAMUX\n",
+    "\n",
+    "---\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "language": "python"
+   },
+   "outputs": [],
+   "source": [
+    "#| echo: false\n",
+    "# from hamux_qmd.core import *"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "> Energy formulation for deep learning\n",
+    "\n",
+    "This file will become your README and also the index of your documentation.\n",
+    "\n",
+    "## Developer Guide\n",
+    "\n",
+    "If you are new to using `nbdev` here are some useful pointers to get you started.\n",
+    "\n",
+    "### Install hamux_qmd in Development mode\n",
+    "\n",
+    "```sh\n",
+    "# make sure hamux_qmd package is installed in development mode\n",
+    "$ pip install -e .\n",
+    "\n",
+    "# make changes under nbs/ directory\n",
+    "# ...\n",
+    "\n",
+    "# compile to have changes apply to hamux_qmd\n",
+    "$ nbdev_prepare"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "language": "python"
+   },
+   "outputs": [],
+   "source": [
+    "## Usage\n",
+    "\n",
+    "### Installation\n",
+    "\n",
+    "Install latest from the GitHub [repository][repo]:\n",
+    "\n",
+    "```sh\n",
+    "$ pip install git+https://github.com/bhoov/hamux_qmd.git"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "or from [conda][conda]\n",
+    "\n",
+    "```sh\n",
+    "$ conda install -c bhoov hamux_qmd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "language": "python"
+   },
+   "outputs": [],
+   "source": [
+    "or from [pypi][pypi]\n",
+    "\n",
+    "\n",
+    "```sh\n",
+    "$ pip install hamux_qmd"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "[repo]: https://github.com/bhoov/hamux_qmd\n",
+    "[docs]: https://bhoov.github.io/hamux_qmd/\n",
+    "[pypi]: https://pypi.org/project/hamux_qmd/\n",
+    "[conda]: https://anaconda.org/bhoov/hamux_qmd\n",
+    "\n",
+    "## How to use\n",
+    "\n",
+    "Fill me in please! Don't forget code examples:\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "language": "python"
+   },
+   "outputs": [],
+   "source": [
+    "1+1"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

index_ipynb.ipynb

@@ -0,0 +1,112 @@
+{
+ "cells": [
+  {
+   "cell_type": "raw",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "output-file: index_ipynb.html\n",
+    "title: HAMUX2\n",
+    "\n",
+    "---\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "language": "python"
+   },
+   "outputs": [],
+   "source": [
+    "#| echo: false\n",
+    "# from hamux_qmd.core import *"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "> Energy formulation for deep learning\n",
+    "\n",
+    "This file will become your README and also the index of your documentation.\n",
+    "\n",
+    "## Developer Guide\n",
+    "\n",
+    "If you are new to using `nbdev` here are some useful pointers to get you started.\n",
+    "\n",
+    "### Install hamux_qmd in Development mode\n",
+    "\n",
+    "```sh\n",
+    "# make sure hamux_qmd package is installed in development mode\n",
+    "$ pip install -e .\n",
+    "\n",
+    "# make changes under nbs/ directory\n",
+    "# ...\n",
+    "\n",
+    "# compile to have changes apply to hamux_qmd\n",
+    "$ nbdev_prepare\n",
+    "```\n",
+    "\n",
+    "## Usage\n",
+    "\n",
+    "### Installation\n",
+    "\n",
+    "Install latest from the GitHub [repository][repo]:\n",
+    "\n",
+    "```sh\n",
+    "$ pip install git+https://github.com/bhoov/hamux_qmd.git\n",
+    "```\n",
+    "\n",
+    "or from [conda][conda]\n",
+    "\n",
+    "```sh\n",
+    "$ conda install -c bhoov hamux_qmd\n",
+    "```\n",
+    "\n",
+    "or from [pypi][pypi]\n",
+    "\n",
+    "\n",
+    "```sh\n",
+    "$ pip install hamux_qmd\n",
+    "```\n",
+    "\n",
+    "\n",
+    "[repo]: https://github.com/bhoov/hamux_qmd\n",
+    "[docs]: https://bhoov.github.io/hamux_qmd/\n",
+    "[pypi]: https://pypi.org/project/hamux_qmd/\n",
+    "[conda]: https://anaconda.org/bhoov/hamux_qmd\n",
+    "\n",
+    "## How to use\n",
+    "\n",
+    "Fill me in please! Don't forget code examples:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "language": "python"
+   },
+   "outputs": [],
+   "source": [
+    "1+1"
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

nbdev/_modidx.py

@@ -100,7 +100,8 @@
                                    'nbdev.frontmatter._dict2fm': ('api/frontmatter.html#_dict2fm', 'nbdev/frontmatter.py'),
                                    'nbdev.frontmatter._fm2dict': ('api/frontmatter.html#_fm2dict', 'nbdev/frontmatter.py'),
                                    'nbdev.frontmatter._insertfm': ('api/frontmatter.html#_insertfm', 'nbdev/frontmatter.py'),
-                                   'nbdev.frontmatter._md2dict': ('api/frontmatter.html#_md2dict', 'nbdev/frontmatter.py')},
+                                   'nbdev.frontmatter._md2dict': ('api/frontmatter.html#_md2dict', 'nbdev/frontmatter.py'),
+                                   'nbdev.frontmatter._parse_kv_block': ('api/frontmatter.html#_parse_kv_block', 'nbdev/frontmatter.py')},
             'nbdev.imports': {},
             'nbdev.maker': { 'nbdev.maker.ModuleMaker': ('api/maker.html#modulemaker', 'nbdev/maker.py'),
                              'nbdev.maker.ModuleMaker.__init__': ('api/maker.html#modulemaker.__init__', 'nbdev/maker.py'),
@@ -240,13 +241,21 @@
                                   'nbdev.processors.strip_ansi': ('api/processors.html#strip_ansi', 'nbdev/processors.py'),
                                   'nbdev.processors.strip_hidden_metadata': ( 'api/processors.html#strip_hidden_metadata',
                                                                               'nbdev/processors.py')},
-            'nbdev.qmd': { 'nbdev.qmd._install_nbdev': ('api/qmd.html#_install_nbdev', 'nbdev/qmd.py'),
+            'nbdev.qmd': { 'nbdev.qmd._get_fence_ticks': ('api/qmd.html#_get_fence_ticks', 'nbdev/qmd.py'),
+                           'nbdev.qmd._install_nbdev': ('api/qmd.html#_install_nbdev', 'nbdev/qmd.py'),
+                           'nbdev.qmd._nb_to_qmd_str': ('api/qmd.html#_nb_to_qmd_str', 'nbdev/qmd.py'),
+                           'nbdev.qmd._qmd_to_raw_cell': ('api/qmd.html#_qmd_to_raw_cell', 'nbdev/qmd.py'),
                            'nbdev.qmd.btn': ('api/qmd.html#btn', 'nbdev/qmd.py'),
                            'nbdev.qmd.div': ('api/qmd.html#div', 'nbdev/qmd.py'),
                            'nbdev.qmd.img': ('api/qmd.html#img', 'nbdev/qmd.py'),
+                           'nbdev.qmd.ipynb_to_qmd': ('api/qmd.html#ipynb_to_qmd', 'nbdev/qmd.py'),
                            'nbdev.qmd.meta': ('api/qmd.html#meta', 'nbdev/qmd.py'),
+                           'nbdev.qmd.read_nb_or_qmd': ('api/qmd.html#read_nb_or_qmd', 'nbdev/qmd.py'),
+                           'nbdev.qmd.read_qmd': ('api/qmd.html#read_qmd', 'nbdev/qmd.py'),
                            'nbdev.qmd.tbl_row': ('api/qmd.html#tbl_row', 'nbdev/qmd.py'),
-                           'nbdev.qmd.tbl_sep': ('api/qmd.html#tbl_sep', 'nbdev/qmd.py')},
+                           'nbdev.qmd.tbl_sep': ('api/qmd.html#tbl_sep', 'nbdev/qmd.py'),
+                           'nbdev.qmd.write_nb_or_qmd': ('api/qmd.html#write_nb_or_qmd', 'nbdev/qmd.py'),
+                           'nbdev.qmd.write_qmd': ('api/qmd.html#write_qmd', 'nbdev/qmd.py')},
             'nbdev.quarto': { 'nbdev.quarto.IndentDumper': ('api/quarto.html#indentdumper', 'nbdev/quarto.py'),
                               'nbdev.quarto.IndentDumper.increase_indent': ( 'api/quarto.html#indentdumper.increase_indent',
                                                                              'nbdev/quarto.py'),
@@ -281,6 +290,27 @@
                               'nbdev.quarto.nbdev_sidebar': ('api/quarto.html#nbdev_sidebar', 'nbdev/quarto.py'),
                               'nbdev.quarto.prepare': ('api/quarto.html#prepare', 'nbdev/quarto.py'),
                               'nbdev.quarto.refresh_quarto_yml': ('api/quarto.html#refresh_quarto_yml', 'nbdev/quarto.py')},
+            'nbdev.read': { 'nbdev.read._apply_defaults': ('api/config.html#_apply_defaults', 'nbdev/read.py'),
+                            'nbdev.read._basic_export_nb': ('api/config.html#_basic_export_nb', 'nbdev/read.py'),
+                            'nbdev.read._cfg2txt': ('api/config.html#_cfg2txt', 'nbdev/read.py'),
+                            'nbdev.read._fetch_from_git': ('api/config.html#_fetch_from_git', 'nbdev/read.py'),
+                            'nbdev.read._get_info': ('api/config.html#_get_info', 'nbdev/read.py'),
+                            'nbdev.read._git_repo': ('api/config.html#_git_repo', 'nbdev/read.py'),
+                            'nbdev.read._has_py': ('api/config.html#_has_py', 'nbdev/read.py'),
+                            'nbdev.read._nbdev_config_file': ('api/config.html#_nbdev_config_file', 'nbdev/read.py'),
+                            'nbdev.read._prompt_user': ('api/config.html#_prompt_user', 'nbdev/read.py'),
+                            'nbdev.read._type': ('api/config.html#_type', 'nbdev/read.py'),
+                            'nbdev.read._xdg_config_paths': ('api/config.html#_xdg_config_paths', 'nbdev/read.py'),
+                            'nbdev.read.add_init': ('api/config.html#add_init', 'nbdev/read.py'),
+                            'nbdev.read.config_key': ('api/config.html#config_key', 'nbdev/read.py'),
+                            'nbdev.read.create_output': ('api/config.html#create_output', 'nbdev/read.py'),
+                            'nbdev.read.get_config': ('api/config.html#get_config', 'nbdev/read.py'),
+                            'nbdev.read.is_nbdev': ('api/config.html#is_nbdev', 'nbdev/read.py'),
+                            'nbdev.read.nbdev_create_config': ('api/config.html#nbdev_create_config', 'nbdev/read.py'),
+                            'nbdev.read.show_src': ('api/config.html#show_src', 'nbdev/read.py'),
+                            'nbdev.read.update_proj': ('api/config.html#update_proj', 'nbdev/read.py'),
+                            'nbdev.read.update_version': ('api/config.html#update_version', 'nbdev/read.py'),
+                            'nbdev.read.write_cells': ('api/config.html#write_cells', 'nbdev/read.py')},
             'nbdev.release': { 'nbdev.release.Release': ('api/release.html#release', 'nbdev/release.py'),
                                'nbdev.release.Release.__init__': ('api/release.html#release.__init__', 'nbdev/release.py'),
                                'nbdev.release.Release._issue_groups': ('api/release.html#release._issue_groups', 'nbdev/release.py'),
@@ -365,4 +395,5 @@
                             'nbdev.sync.nbdev_update': ('api/sync.html#nbdev_update', 'nbdev/sync.py')},
             'nbdev.test': { 'nbdev.test._keep_file': ('api/test.html#_keep_file', 'nbdev/test.py'),
                             'nbdev.test.nbdev_test': ('api/test.html#nbdev_test', 'nbdev/test.py'),
+                            'nbdev.test.no_eval': ('api/test.html#no_eval', 'nbdev/test.py'),
                             'nbdev.test.test_nb': ('api/test.html#test_nb', 'nbdev/test.py')}}}

nbdev/clean.py

@@ -38,7 +38,7 @@ def nbdev_trust(
     path = fname if fname.is_dir() else fname.parent
     check_fname = path/".last_checked"
     last_checked = os.path.getmtime(check_fname) if check_fname.exists() else None
-    nbs = globtastic(fname, file_glob='*.ipynb', skip_folder_re='^[_.]') if fname.is_dir() else [fname]
+    nbs = globtastic(fname, file_re=r'.*\.ipynb$|.*\.qmd$', skip_folder_re='^[_.]') if fname.is_dir() else [fname]
     for fn in nbs:
         if last_checked and not force_all:
             last_changed = os.path.getmtime(fn)
@@ -141,7 +141,7 @@ def nbdev_clean(
     _write = partial(process_write, warn_msg='Failed to clean notebook', proc_nb=_clean)
     if stdin: return _write(f_in=sys.stdin, f_out=sys.stdout)
     if fname is None: fname = get_config().nbs_path
-    for f in globtastic(fname, file_glob='*.ipynb', skip_folder_re='^[_.]'): _write(f_in=f, disp=disp)
+    for f in globtastic(fname, file_re=r'.*\.ipynb$', skip_folder_re='^[_.]'): _write(f_in=f, disp=disp) # Don't clean .qmd files
 
 # %% ../nbs/api/11_clean.ipynb
 def clean_jupyter(path, model, **kwargs):

nbdev/doclinks.py

@@ -116,20 +116,20 @@ def _build_modidx(dest=None, nbs_path=None, skip_exists=False):
 
 # %% ../nbs/api/05_doclinks.ipynb
 @delegates(globtastic)
-def nbglob(path=None, skip_folder_re = '^[_.]', file_glob='*.ipynb', skip_file_re='^[_.]', key='nbs_path', as_path=False, **kwargs):
+def nbglob(path=None, skip_folder_re = '^[_.]', file_re=r'.*\.ipynb$|.*\.qmd$', skip_file_re='^[_.]', key='nbs_path', as_path=False, **kwargs):
     "Find all files in a directory matching an extension given a config key."
     path = Path(path or get_config()[key])
     recursive=get_config().recursive
-    res = globtastic(path, file_glob=file_glob, skip_folder_re=skip_folder_re,
+    res = globtastic(path, file_re=file_re, skip_folder_re=skip_folder_re,
                      skip_file_re=skip_file_re, recursive=recursive, **kwargs)
     return res.map(Path) if as_path else res
 
 # %% ../nbs/api/05_doclinks.ipynb
 def nbglob_cli(
     path:str=None, # Path to notebooks
     symlinks:bool=False, # Follow symlinks?
-    file_glob:str='*.ipynb', # Only include files matching glob
-    file_re:str=None, # Only include files matching regex
+    file_glob:str=None, # Only include files matching glob
+    file_re:str=r'.*\.ipynb$|.*\.qmd$', # Only include files matching regex
     folder_re:str=None, # Only enter folders matching regex
     skip_file_glob:str=None, # Skip files matching glob
     skip_file_re:str='^[_.]', # Skip files matching regex