diff --git a/README.md b/README.md deleted file mode 100644 index 5615aa7..0000000 --- a/README.md +++ /dev/null @@ -1,15 +0,0 @@ -# Data Standards for Environmental Surveillance (dses) - -This is the documentation for the data standards for environmental surveillance, developed by the Data Science Innovation Hub at [ARTPARK](https://artpark.in) at the [Indian Institute of Science](https://iisc.ac.in). - -The aim is to create a set of data standards, along the lines of [FHIR HL7](https://hl7.org/fhir/) that are fast to adopt, interoperable, and can be scaled to any kind of disease while allowing extensibility for any user's sepcific use-case. - -If you are currently on Github - you can find the docs hosted at [dses.dsih.artpark.in](https://dses.dsih.artpark.in). - -## Contributing - -Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms. - -## Credits - -Data Standards for Environmental Surveillance ([`dses`](https://github.com/dsih-artpark/dses)) was created with [`cookiecutter`](https://cookiecutter.readthedocs.io/en/latest/) and the `py-pkgs-cookiecutter` [template](https://github.com/py-pkgs/py-pkgs-cookiecutter). The documentation is rendered using [`sphinx`](https://www.sphinx-doc.org/) and rendered and hosted using [`readthedocs.io`](https://readthedocs.io), and uses [`poetry`](https://python-poetry.org/) to manage dependencies in the rendering scripts. \ No newline at end of file diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..ff8878a --- /dev/null +++ b/README.rst @@ -0,0 +1,20 @@ +#################################################### +Data Standards for Environmental Surveillance (dses) +#################################################### + +.. warning:: + This documentation is under active development and might be changing. Check out our Github to see the latest changes. + +This is the documentation for the data standards for environmental surveillance, developed by the Data Science Innovation Hub at `ARTPARK `_ at the `Indian Institute of Science `_. + +The aim is to create a set of data standards, along the lines of `FHIR HL7 `_ that are fast to adopt, interoperable, and can be scaled to any kind of disease while allowing extensibility for any user's specific use-case. + +Contributing +------------- + +Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms. + +Credits +------------- + +Data Standards for Environmental Surveillance (`dses `_) was created with `cookiecutter `_ and the `py-pkgs-cookiecutter` `template `_. The documentation is rendered using `sphinx `_ and hosted on `readthedocs.io `_, and uses `poetry `_ to manage dependencies in the rendering scripts. diff --git a/docs/conf.py b/docs/conf.py index fc26cde..4e64b8c 100755 --- a/docs/conf.py +++ b/docs/conf.py @@ -35,18 +35,3 @@ # a list of builtin themes. # html_theme = "sphinx_rtd_theme" - -# -- Options for Markdown rendering ------------------------------------------ - -# Add the data_standards directory to the source directory -source_dir = os.path.abspath(os.path.dirname(__file__)) -data_standards_dir = os.path.join(source_dir, "data_standards") - -# Include data_standards directory for Markdown rendering -myst_include_patterns = [data_standards_dir] - -# Recursively include subdirectories of data_standards -myst_include_directories = [data_standards_dir] - -# If you want to customize how files in data_standards are rendered, -# you can do so using the `myst_custom_renderers` setting. diff --git a/docs/data_standards/getting_started.md b/docs/data_standards/getting_started.md new file mode 100644 index 0000000..8b3a794 --- /dev/null +++ b/docs/data_standards/getting_started.md @@ -0,0 +1 @@ +# Getting Started \ No newline at end of file diff --git a/docs/data_standards/index.md b/docs/data_standards/index.md deleted file mode 100644 index ecf2de3..0000000 --- a/docs/data_standards/index.md +++ /dev/null @@ -1,10 +0,0 @@ -# Data Standards - -Welcome to the Data Standards section. - -```{toctree} -:maxdepth: 2 -:glob: - -** -``` diff --git a/docs/data_standards/index.rst b/docs/data_standards/index.rst new file mode 100644 index 0000000..26f61dd --- /dev/null +++ b/docs/data_standards/index.rst @@ -0,0 +1,14 @@ +Data Standards +============== +Welcome to the Data Standards section. + + .. note:: + This section is under active development. + +.. toctree:: + :maxdepth: 2 + :glob: + + getting_started.md + roles/index.md + users/index.md diff --git a/docs/index.md b/docs/index.md deleted file mode 100755 index 79fe3e7..0000000 --- a/docs/index.md +++ /dev/null @@ -1,13 +0,0 @@ -```{include} ../README.md -``` - -```{toctree} -:maxdepth: 2 -:glob: - -data_standards/* -example.ipynb -changelog.md -contributing.md -conduct.md -``` \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst new file mode 100755 index 0000000..da438d1 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,35 @@ +#################################################### +Data Standards for Environmental Surveillance (dses) +#################################################### + +.. warning:: + This documentation is under active development and might be changing. Check out our Github to see the latest changes. + +This is the documentation for the data standards for environmental surveillance, developed by the Data Science Innovation Hub at `ARTPARK `_ at the `Indian Institute of Science `_. + +The aim is to create a set of data standards, along the lines of `FHIR HL7 `_ that are fast to adopt, interoperable, and can be scaled to any kind of disease while allowing extensibility for any user's specific use-case. + +If you are currently on Github - you can find the docs hosted at `dses.dsih.artpark.in `_. + + +Table of Contents +----------------- + +.. toctree:: + :maxdepth: 2 + + data_standards/index.md + example.ipynb + changelog.md + contributing.md + conduct.md + +Contributing +------------- + +Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms. + +Credits +------------- + +Data Standards for Environmental Surveillance (`dses `_) was created with `cookiecutter `_ and the `py-pkgs-cookiecutter` `template `_. The documentation is rendered using `sphinx `_ and hosted on `readthedocs.io `_, and uses `poetry `_ to manage dependencies in the rendering scripts. diff --git a/poetry.lock b/poetry.lock index 71c486b..861cb8a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2158,4 +2158,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "d116a45055d08141db6f8e03e64b11ccc61b8a14a929df37c19a0296a9ee80a8" +content-hash = "3b2285d793c6858c476db64a17238d7703cdd0715df6dbb1c10a86ff1daf8a22" diff --git a/pyproject.toml b/pyproject.toml index 213ce9a..bca49ac 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,9 +9,10 @@ readme = "README.md" [tool.poetry.dependencies] python = "^3.9" -[tool.poetry.dev-dependencies] - [tool.poetry.group.dev.dependencies] +pyyaml = "^6.0.1" + +[tool.poetry.group.docs.dependencies] myst-nb = {version = "^1.1.0", python = "^3.9"} sphinx-autoapi = "^3.0.0" sphinx-rtd-theme = "^2.0.0"