Started writing documentation

8 files changed, 205 insertions, 0 deletions

diff --git a/docs/Makefile b/docs/Makefile
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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/deploy.sh b/docs/deploy.sh
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+tar czvf build.tar.gz build/
+scp build.tar.gz eden@vps.eda.gay:/home/eden/SmarkerDocs/build.tar.gz
+rm build.tar.gz
+ssh eden@vps.eda.gay "rm -rf /home/eden/SmarkerDocs/build/"
+ssh eden@vps.eda.gay "tar xvf /home/eden/SmarkerDocs/build.tar.gz -C /home/eden/SmarkerDocs"
+ssh eden@vps.eda.gay "rm /home/eden/SmarkerDocs/build.tar.gz"
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diff --git a/docs/source/conf.py b/docs/source/conf.py
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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath(os.path.join("..", "..", "Smarker")))
+# print(os.listdir(os.path.abspath(os.path.join("..", "..", "Smarker"))))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'Smarker'
+copyright = '2022, Eden Attenborough'
+author = 'Eden Attenborough'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.coverage', 'sphinx.ext.napoleon']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
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diff --git a/docs/source/configfile.rst b/docs/source/configfile.rst
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+++ b/docs/source/configfile.rst
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+.. _configfile:
+
+``smarker.conf``: Configuration File
+====================================
+
+Here is what it should look like. It needs to be in the same directory as the 
+source code. Its a standard .ini format.
+
+Once it's been created, you can safely forget about it since all of the options 
+can be over-ridden in command line arguments.::
+    
+    [mysql]
+    host = vps.eda.gay
+    port = 3307
+    user = root
+    passwd = ************
+
+    [tex]
+    columns = 1
+    show_full_docs = True
+    show_source = True
+    show_all_regex_occurrences = True
+    show_all_run_output = True
+
+    [md]
+    show_full_docs = False
+    show_source = False
+    show_all_regex_occurrences = True
+    show_all_run_output = False
+
+    [txt]
+    show_full_docs = False
+    show_source = False
+    show_all_regex_occurrences = True
+    show_all_run_output = False
+
+The first block configures where your SQL server is. The other options are
+the default options when generating reports. ``[tex]`` options are inherited
+for rendering to PDF.
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diff --git a/docs/source/database.rst b/docs/source/database.rst
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+``database.py``: Interfacing with the database
+==============================================
+
+.. automodule:: database
+    :members:
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diff --git a/docs/source/docker.rst b/docs/source/docker.rst
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+++ b/docs/source/docker.rst
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+.. _docker:
+
+Running in docker
+=================
+
+Running the system in docker has many advantages:
+
+* Don't have to worry about getting dependencies- the system requires many libraries to be avaliable on the PATH
+
+* Isolation: we are running remote code supplied by anyone, which can potentially be very dangerous. Docker isolates the dangerous code, a significant security concern
+
+* Makes the system be able to be used in Windows- Smarker has been tested in docker for windows using WSL for the backend
+
+Using docker
+------------
+
+We have a ``Dockerfile`` ready for use: ``sudo docker build -t smarker .``
+
+To input files and get the output report we use docker volumes ``-v``. Unfortunately
+docker seems to be rather buggy passing through single files, so we recommend making
+a directory to pass through instead. 
+
+Command line arguments can be replaced with environment variables, using the ``-e``
+flag in a ``key=value`` format. There is the additional environment variable ``SMARKERDEPS``
+which will pip install pypi modules at the start, deliminated with commas.
+
+.. code-block:: bash
+    
+    sudo docker run \
+        -v "$(pwd)/../wsData.txt":/wsData.txt \
+        -v "$(pwd)/100301654.zip":/tmp/100301654.zip \
+        -v "$(pwd)/out/":/out/ \
+        -e submission=/tmp/100301654.zip \
+        -e assessment=example \
+        -e SMARKERDEPS=matplotlib \
+        -e format=pdf \
+        -e output=/out/100301654.pdf \
+        --rm smarker
+
+To list assessments in the database using docker:
+
+.. code-block:: bash
+    
+    sudo docker run -it --entrypoint python --rm smarker assessments.py --list yes
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diff --git a/docs/source/index.rst b/docs/source/index.rst
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+Welcome to Smarker's documentation!
+===================================
+
+Setting up
+----------
+
+* Set up a MySQL/MariaDB server. The database will be generated automatically.
+* Add ``smarker.conf`` to the root directory of the code. See :ref:`configfile` for the structure of this file.
+* Decide how you want to run the program: with or without docker.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Modules:
+   
+   reflect.rst
+   database.rst
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Other Pages:
+
+   configfile.rst
+   docker.rst
+
+
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/source/reflect.rst b/docs/source/reflect.rst
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+``reflect.py``: Getting information about code
+==============================================
+
+.. automodule:: reflect
+    :members:
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