Merge branch 'develop' into 'master'

v0.3.0

Closes #22

See merge request !17

.dockerignore

+*
+!pyproject.toml

.gitignore

@@ -15,3 +15,4 @@ tests/notebooks
 *.egg-info/
 dist/
 poetry.lock
+.venv

.gitlab-ci.yml

-image: boileaum/jupyter
-
 variables:
   GIT_SUBMODULE_STRATEGY: recursive
 
 stages:
+  - deps
   - test
   - deploy
 
-before_script:
-    - curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
-    - source $HOME/.poetry/env
+deps:
+  stage: deps
+  tags:
+    - shell
+  script:
+    - docker login -u gitlab-ci-token -p $CI_JOB_TOKEN $CI_REGISTRY
+    - docker info
+    - echo "Building $CI_REGISTRY_IMAGE"
+    - DOCKER_BUILDKIT=1 docker build --pull -t $CI_REGISTRY_IMAGE -f Dockerfile .
+    - docker push $CI_REGISTRY_IMAGE
 
 test:
   stage: test
+  image: $CI_REGISTRY_IMAGE
   tags:
     - docker
   script:
@@ -21,6 +28,7 @@ test:
 
 deploy:
   stage: deploy
+  image: $CI_REGISTRY_IMAGE
   tags:
     - docker
   script:

CHANGELOG.md

+# Changelog
+
+## [0.3.0] - 2020-11-05
+
+### Changed
+
+- `style_ipython.tplx` -> `style_ipython.tex.j2` in `/theme/default/templates/book.tplx`. Please update this file in your local `theme/` dir if you are using nbconvert >= 6.0
+- some code enhancement
+
+### Fixed
+
+- Fix issues with pdf generation using nbconvert >= 6.0

Dockerfile

+FROM boileaum/jupyter
+
+# From Jupyter Project <jupyter@googlegroups.com>
+
+LABEL maintainer="Matthieu Boileau <matthieu.boileau@math.unistra.fr>"
+
+COPY pyproject.toml .
+RUN curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
+ENV PATH="$HOME/.poetry/bin:$PATH"
+RUN poetry install
\ No newline at end of file

nbcourse/__init__.py

-"""
-Build a small website to host Jupyter notebooks as course chapters
-"""
+import logging
 
-import argparse
-from .nbcourse import NbCourse, DEFAULT_CONFIG_FILE
-from .initialize import initialize
-from pathlib import Path
-from .mydoit import MyDoitHelp, ClassTaskLoader
-
-
-def get_help_epilog() -> str:
-    """Instanciate a minimal nbcourse to return help string"""
-    course = NbCourse()
-    loader = ClassTaskLoader(course)
-    return MyDoitHelp(task_loader=loader).get_help()
-
-
-def main():
-    """CLI for nbcourse"""
-
-    prog = globals()['__package__']
-    description = globals()['__doc__']
-    formatter = argparse.RawDescriptionHelpFormatter
-    epilog = get_help_epilog()
-
-    parser = argparse.ArgumentParser(prog=prog,
-                                     description=description,
-                                     formatter_class=formatter,
-                                     epilog=epilog)
-    init = parser.add_argument_group('initialize')
-    init.add_argument('--init', action='store_true',
-                      help=initialize.__doc__)
-    generate = parser.add_argument_group('generate')
-    generate.add_argument('--config', dest='config_file', type=Path,
-                          default=DEFAULT_CONFIG_FILE,
-                          help='Load YAML file describing site configuration '
-                               '(default: %(default)s)')
-
-    # Handle undefined arguments
-    parsed, extra = parser.parse_known_args()
-
-    if parsed.init:
-        initialize()
-    else:
-        course = NbCourse(parsed.config_file)
-        course.build(extra)
+log = logging.getLogger(__name__)
+logging.basicConfig(level=logging.INFO)

nbcourse/__main__.py

@@ -2,7 +2,7 @@
 python -m nbcourse module entry point to run via python -m
 """
 
-from . import main
+from .main import main
 
 
 if __name__ == '__main__':

nbcourse/book.py

 import jinja2
-import logging
+from . import log
 import os
 from bookbook.latex import combine_and_convert
 from pathlib import Path
 
-logging.basicConfig(level=logging.INFO)
-log = logging.getLogger(__name__)
-
 
 class BookContext:
     """

nbcourse/main.py

+"""
+Build a small website to host Jupyter notebooks as course chapters
+"""
+
+import argparse
+from .nbcourse import NbCourse, DEFAULT_CONFIG_FILE
+from .initialize import initialize
+from pathlib import Path
+from .mydoit import MyDoitHelp, ClassTaskLoader
+
+
+def get_help_epilog() -> str:
+    """Instanciate a minimal nbcourse to return help string"""
+    course = NbCourse()
+    loader = ClassTaskLoader(course)
+    return MyDoitHelp(task_loader=loader).get_help()
+
+
+def main():
+    """CLI for nbcourse"""
+
+    prog = globals()['__package__']
+    description = globals()['__doc__']
+    formatter = argparse.RawDescriptionHelpFormatter
+    epilog = get_help_epilog()
+
+    parser = argparse.ArgumentParser(prog=prog,
+                                     description=description,
+                                     formatter_class=formatter,
+                                     epilog=epilog)
+    init = parser.add_argument_group('initialize')
+    init.add_argument('--init', action='store_true',
+                      help=initialize.__doc__)
+    generate = parser.add_argument_group('generate')
+    generate.add_argument('--config', dest='config_file', type=Path,
+                          default=DEFAULT_CONFIG_FILE,
+                          help='Load YAML file describing site configuration '
+                               '(default: %(default)s)')
+
+    parser.add_argument('--verbosity', '-v', type=str, )
+    # Handle undefined arguments
+    parsed, extra = parser.parse_known_args()
+
+    if parsed.init:
+        initialize()
+    else:
+        course = NbCourse(parsed.config_file)
+        course.build(extra)

nbcourse/nbcourse.py

@@ -8,6 +8,7 @@ Define a NbCourse object containing:
 from pathlib import Path, PosixPath
 import yaml
 from doit.tools import create_folder, config_changed
+from . import log
 from .utils import update_material, clean_tree, get_file_list, update_dict, \
     zip_files
 from .pages import HomePage, MarkdownPage
@@ -16,11 +17,8 @@ import nbformat
 from nbconvert.preprocessors import ExecutePreprocessor
 from nbconvert import HTMLExporter, SlidesExporter
 from .mydoit import MyDoitMain, ClassTaskLoader
-import logging
 import sys
 
-log = logging.getLogger(__name__)
-logging.basicConfig(level=logging.INFO)
 
 DEFAULT_CONFIG_FILE = "nbcourse.yml"
 
@@ -28,39 +26,39 @@ DEFAULT_CONFIG_FILE = "nbcourse.yml"
 class NbCourse:
 
     default_conf = {
-                    'theme': {
-                        'dir': 'theme/default',
-                        'material': ('css', 'img')
-                        },
-                    'nb': {
-                        'dir': '.',
-                        'timeout': 60,
-                        'material': ()
-                        },
-                    'pages': {
-                        'dir': 'pages',
-                        'home': 'index.html'
-                        },
-                    'book': {
-                        'titlepage': 'titlepage.tex',
-                        'file': None,
-                        },
-                    'local_reveal': False,
-                    'slug_title': 'course',
-                    'output_dir': 'build',
-                    'title': 'A course',
-                    'subtitle': None,
-                    'favicon': None,
-                    'picture': None,
-                    'authors': [],
-                    'chapter_preview_only': [],
-                    'license': None,
-                    'links': {'manual': {
-                                    'title': 'Manual',
-                                    'target': 'manual.html',
-                                    }
-                              }
-                    }
+        'theme': {
+            'dir': 'theme/default',
+            'material': ('css', 'img')
+        },
+        'nb': {
+            'dir': '.',
+            'timeout': 60,
+            'material': ()
+        },
+        'pages': {
+            'dir': 'pages',
+            'home': 'index.html'
+        },
+        'book': {
+            'titlepage': 'titlepage.tex',
+            'file': None,
+        },
+        'local_reveal': False,
+        'slug_title': 'course',
+        'output_dir': 'build',
+        'title': 'A course',
+        'subtitle': None,
+        'favicon': None,
+        'picture': None,
+        'authors': [],
+        'chapter_preview_only': [],
+        'license': None,
+        'links': {'manual': {
+            'title': 'Manual',
+            'target': 'manual.html',
+        }
+        }
+    }
 
     def __init__(self, user_conf=None):
         """Build from user_conf"""
@@ -72,12 +70,12 @@ class NbCourse:
             self.conf[key]['material_paths'] = [
                 self.conf[key]['path'] / Path(d)
                 for d in self.conf[key]['material']
-                ]
+            ]
         self.conf['pages']['path'] = Path(self.conf['pages']['dir'])
         self.conf['output_path'] = Path(self.conf['output_dir'])
         if self.conf['local_reveal']:
             self.conf['reveal_path'] = Path(__file__).parent / \
-                                       Path('reveal.js')
+                Path('reveal.js')
         self.notebooks = tuple(self.conf['nb']['path'].glob('*-*.ipynb'))
         if user_conf and not self.notebooks:
             log.error("""

nbcourse/pages.py

+from . import log
 import nbformat
 import re
-import logging
 import markdown
 from pathlib import Path
 from pprint import pformat
@@ -9,9 +9,6 @@ from bs4 import BeautifulSoup
 import frontmatter
 import sys
 
-log = logging.getLogger(__name__)
-logging.basicConfig(level=logging.INFO)
-
 
 class Page:
     """An abstract class for a static web page"""
@@ -64,7 +61,7 @@ class HomePage(Page):
         nb = nbformat.read(str(path), as_version=4)
 
         if nb.cells[0].cell_type != 'markdown':
-            log.error(f"The first cell of the notebook {path} should be Markdown type " + 
+            log.error(f"The first cell of the notebook {path} should be Markdown type " +
                       f"({nb.cells[0].cell_type} instead).")
             sys.exit()
         lines = nb.cells[0].source.splitlines()

nbcourse/skeleton/theme/default/templates/book.tplx

 % Default to the notebook output style
 ((* if not cell_style is defined *))
-    ((* set cell_style = 'style_ipython.tplx' *))
+    ((* set cell_style = 'style_ipython.tex.j2' *))
 ((* endif *))
 
 % Inherit from the specified cell style.

pyproject.toml

 [tool.poetry]
 name = "nbcourse"
-version = "0.2.6"
+version = "0.3.0"
 description = "Create a minisite to publish a course based on Jupyter notebooks"
 authors = ["Matthieu Boileau <matthieu.boileau@math.unistra.fr>"]
 license = "MIT"
@@ -10,8 +10,7 @@ readme = "README.md"
 
 [tool.poetry.dependencies]
 python = "^3.7"
-nbconvert = "^5.6.1"
-bookbook = "^0.2"
+nbconvert = ">=6.0"
 bs4 = "^0.0.1"
 IPython = "^7.15.0"
 jinja2 = "^2.11.2"
@@ -22,6 +21,7 @@ rise = "^5.6.1"
 pyyaml = "^5.3.1"
 doit = ">=0.32.0"
 python-frontmatter = "^0.5.0"
+bookbook = { git = "https://github.com/boileaum/bookbook.git", branch = "master" }
 
 [tool.poetry.dev-dependencies]
 pytest = "^5.4.3"

requirements.txt

-appnope==0.1.0; sys_platform == "darwin" or platform_system == "Darwin"
-attrs==19.3.0
+appnope==0.1.0; sys_platform == "darwin" and platform_system == "Darwin"
+argon2-cffi==20.1.0
+async-generator==1.10; python_version >= "3.5"
+attrs==20.3.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
 backcall==0.2.0
-beautifulsoup4==4.9.1
-bleach==3.1.5
-bookbook==0.2
+beautifulsoup4==4.9.3
+bleach==3.2.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
+bookbook @ git+https://github.com/boileaum/bookbook.git@master ; python_version >= "3.5"
 bs4==0.0.1
-cloudpickle==1.4.1
-colorama==0.4.3; sys_platform == "win32"
+cffi==1.14.3
+cloudpickle==1.6.0; python_version >= "3.5"
+colorama==0.4.4; python_version >= "2.7" and python_full_version < "3.0.0" and sys_platform == "win32" or python_full_version >= "3.5.0" and sys_platform == "win32"
 data==0.4
-decorator==4.4.2
-defusedxml==0.6.0
-doit==0.32.0
-entrypoints==0.3
+decorator==4.4.2; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.2.0"
+defusedxml==0.6.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
+doit==0.33.1; python_version >= "3.5"
+entrypoints==0.3; python_version >= "2.7"
 funcsigs==1.0.2
-future==0.18.2
-importlib-metadata==1.6.1; python_version < "3.8"
-ipykernel==5.3.0
-ipython==7.15.0
+future==0.18.2; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
+importlib-metadata==2.0.0; python_version >= "2.7" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.5.0" and python_version < "3.8"
+ipykernel==5.3.4; python_version >= "3.5"
 ipython-genutils==0.2.0
-jedi==0.17.0
-jinja2==2.11.2
+ipython==7.19.0; python_version >= "3.7"
+jedi==0.17.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
+jinja2==2.11.2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
 jsonschema==3.2.0
-jupyter-client==6.1.3
+jupyter-client==6.1.7; python_version >= "3.5"
 jupyter-contrib-core==0.3.3
 jupyter-contrib-nbextensions==0.5.1
-jupyter-core==4.6.3
+jupyter-core==4.6.3; python_version >= "2.7" and python_version < "3.0" or python_version > "3.0" and python_version < "3.1" or python_version > "3.1" and python_version < "3.2" or python_version > "3.2" and python_version < "3.3" or python_version > "3.3" and python_version < "3.4" or python_version > "3.4"
 jupyter-highlight-selected-word==0.2.0
 jupyter-latex-envs==1.4.6
 jupyter-nbextensions-configurator==0.4.1
+jupyterlab-pygments==0.1.2
 latex==0.7.0
-lxml==4.5.1
+lxml==4.6.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0"
 macfsevents==0.8.1; sys_platform == "darwin"
-markdown==3.2.2
-markupsafe==1.1.1
+markdown==3.3.3; python_version >= "3.6"
+markupsafe==1.1.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
 mistune==0.8.4
-nbconvert==5.6.1
-nbformat==5.0.7
-notebook==6.0.3
-packaging==20.4
-pandocfilters==1.4.2
-parso==0.7.0
+nbclient==0.5.1; python_version >= "3.6"
+nbconvert==6.0.7; python_version >= "3.6"
+nbformat==5.0.8; python_version >= "3.5"
+nest-asyncio==1.4.2; python_version >= "3.5"
+notebook==6.1.4; python_version >= "3.5"
+packaging==20.4; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+pandocfilters==1.4.3; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+parso==0.7.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
 pexpect==4.8.0; sys_platform != "win32"
 pickleshare==0.7.5
 prometheus-client==0.8.0
-prompt-toolkit==3.0.5
-ptyprocess==0.6.0; sys_platform != "win32" or os_name != "nt"
-pygments==2.6.1
+prompt-toolkit==3.0.8; python_full_version >= "3.6.1"
+ptyprocess==0.6.0; sys_platform != "win32" and os_name != "nt"
+pycparser==2.20; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
+pygments==2.7.2; python_version >= "3.5"
 pyinotify==0.9.6; sys_platform == "linux"
-pyparsing==2.4.7
-pyrsistent==0.16.0
-python-dateutil==2.8.1
+pyparsing==2.4.7; python_version >= "2.6" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
+pyrsistent==0.17.3; python_version >= "3.5"
+python-dateutil==2.8.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
 python-frontmatter==0.5.0
 pywin32==228; sys_platform == "win32"
 pywinpty==0.5.7; os_name == "nt"
-pyyaml==5.3.1
-pyzmq==19.0.1
-rise==5.6.1
+pyyaml==5.3.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+pyzmq==19.0.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
+rise==5.7.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0" and python_version < "4")
 send2trash==1.5.0
 shutilwhich==1.1.0
-six==1.15.0
-soupsieve==1.9.6
+six==1.15.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0"
+soupsieve==2.0.1; python_version >= "3.5"
 tempdir==0.7.1
-terminado==0.8.3
+terminado==0.9.1; python_version >= "3.6"
 testpath==0.4.4
-tornado==6.0.4
-traitlets==4.3.3
-wcwidth==0.2.4
+tornado==6.1; python_version >= "3.5"
+traitlets==5.0.5; python_version >= "3.7"
+wcwidth==0.2.5
 webencodings==0.5.1
-zipp==3.1.0; python_version < "3.8"
+zipp==3.4.0; python_version >= "3.6" and python_version < "3.8"

tests/test_nbcourse.py

 from nbcourse.initialize import initialize
 from nbcourse.nbcourse import NbCourse, MyDoitMain, ClassTaskLoader
 from nbcourse.utils import get_functions
-from nbcourse import get_help_epilog
+from nbcourse.main import get_help_epilog
 import pytest
 from pathlib import Path
 import os
@@ -32,14 +32,17 @@ def _create_project(tmpdir, sample=Path('sample')):
     yaml_file.unlink()
     yaml_file.symlink_to(TESTS_PATH / sample / 'nbcourse.yml')
 
+
 @pytest.fixture
 def create_project(tmpdir):
     _create_project(tmpdir)
 
+
 @pytest.fixture
 def create_wrong_project(tmpdir):
     _create_project(tmpdir, sample=Path('wrong_sample'))
 
+
 def test_minimal_nbcourse(create_project):
     """Only test nbcourse object instantiation"""
     NbCourse()