Merge pull request #9 from pepkit/dev

v0.0.5

.gitignore

@@ -78,3 +78,6 @@ peppy.egg-info/
 #ipynm checkpoints
 *ipynb_checkpoints*
 *.egg-info*
+
+# mkdocs website
+site

README.md

@@ -6,7 +6,7 @@
 
 [PEP](http://pepkit.github.io) validation tool based on [`jsonschema`](https://github.com/Julian/jsonschema) package.
 
-See [this jupyter notebook](docs/demo.ipynb) for usage demonstration
+See [this jupyter notebook](docs_jupyter/demo.ipynb) for usage demonstration
 
 ---
 *Eidos* is a Greek term meaning "form" "essence", "type" or "species". See Plato's theory of Forms and Aristotle's theory of universals

docs/README.md

@@ -0,0 +1,10 @@
+# eido
+
+[![Build Status](https://travis-ci.org/pepkit/eido.svg?branch=master)](https://travis-ci.org/pepkit/eido)
+[![Coverage Status](https://coveralls.io/repos/github/pepkit/eido/badge.svg?branch=master)](https://coveralls.io/github/pepkit/eido?branch=master)
+[![PEP compatible](http://pepkit.github.io/img/PEP-compatible-green.svg)](http://pepkit.github.io)
+
+[PEP](http://pepkit.github.io) validation tool based on [`jsonschema`](https://github.com/Julian/jsonschema) package.
+
+---
+*Eidos* is a Greek term meaning "form" "essence", "type" or "species". See Plato's theory of Forms and Aristotle's theory of universals

docs/autodoc_build/eido.md

@@ -0,0 +1,78 @@
+<script>
+document.addEventListener('DOMContentLoaded', (event) => {
+  document.querySelectorAll('h3 code').forEach((block) => {
+    hljs.highlightBlock(block);
+  });
+});
+</script>
+
+<style>
+h3 .content { 
+    padding-left: 22px;
+    text-indent: -15px;
+ }
+h3 .hljs .content {
+    padding-left: 20px;
+    margin-left: 0px;
+    text-indent: -15px;
+    martin-bottom: 0px;
+}
+h4 .content, table .content, p .content, li .content { margin-left: 30px; }
+h4 .content { 
+    font-style: italic;
+    font-size: 1em;
+    margin-bottom: 0px;
+}
+
+</style>
+
+
+# Package `eido` Documentation
+
+```python
+def validate_project(project, schema, exclude_case=False)
+```
+
+Validate a project object against a schema
+#### Parameters:
+
+- `project` (`peppy.Sample`):  a project object to validate
+- `schema` (`str | dict`):  schema dict to validate against or a path to one
+- `exclude_case` (`bool`):  whether to exclude validated objects from the error.Useful when used ith large projects
+
+
+
+
+```python
+def validate_sample(project, sample_name, schema, exclude_case=False)
+```
+
+Validate the selected sample object against a schema
+#### Parameters:
+
+- `project` (`peppy.Project`):  a project object to validate
+- `sample_name` (`str | int`):  name or index of the sample to validate
+- `schema` (`str | dict`):  schema dict to validate against or a path to one
+- `exclude_case` (`bool`):  whether to exclude validated objects from the error.Useful when used ith large projects
+
+
+
+
+```python
+def validate_config(project, schema, exclude_case=False)
+```
+
+Validate the config part of the Project object against a schema
+#### Parameters:
+
+- `project` (`peppy.Project`):  a project object to validate
+- `schema` (`str | dict`):  schema dict to validate against or a path to one
+- `exclude_case` (`bool`):  whether to exclude validated objects from the error.Useful when used ith large projects
+
+
+
+
+
+
+
+*Version Information: `eido` v0.0.5-dev, generated by `lucidoc` v0.4.2*

docs/changelog.md

@@ -2,6 +2,11 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format. 
 
+## [0.0.5] - 2020-02-04
+### Added 
+- [documentation website](http://eido.databio.org/en/latest/)
+- include version in the CLI help
+
 ## [0.0.4] - 2020-01-31
 ### Added
 - `validate_sample` function for sample level validation

docs/contributing.md

@@ -0,0 +1,6 @@
+## Contributing
+
+Pull requests or issues are welcome. After adding a new feature, please add tests in the `tests` folder and run the test suite. The only additional dependencies needed beyond those for the package can be installed with: `pip install -r requirements/requirements-dev.txt`.
+
+Once those are installed, run the tests with `pytest` or `python setup.py test`.
+

docs/install.md

@@ -0,0 +1,14 @@
+# Installing eido
+
+Install from [GitHub releases](https://github.com/pepkit/eido/releases) or from PyPI using `pip`:
+
+- `pip install --user eido`: install into user space.
+- `pip install --user --upgrade eido`: update in user space.
+- `pip install eido`: install into an active virtual environment.
+- `pip install --upgrade eido`: update in virtual environment.
+
+See if your install worked by calling `eidp -h` on the command line. If the `eido` executable in not in your `$PATH`, append this to your `.bashrc` or `.profile` (or `.bash_profile` on macOS):
+
+```{console}
+export PATH=~/.local/bin:$PATH
+```

docs/jupyter_docs/cli.md

@@ -0,0 +1,51 @@
+jupyter:True
+# `eido` command line usage
+
+To use the command line application one just needs two required paths as arguments to the `eido` command:
+
+- a path to a project configuration file (`-p`/`--pep` option)
+- a path to a YAML formatted schema (`-s`/`--schema` option)
+
+Optionally, to validate just the config part of the PEP or a specific sample, `-n`/`--sample-name` or `-c`/`--just-config` arguments should be used, respectively. Please refer to the help for more details:
+
+```
+~ eido -h
+```
+```
+version: 0.0.5
+usage: eido [-h] [-V] -p PEP -s SCHEMA [-e] [-n SAMPLE_NAME | -c] [--silent]
+            [--verbosity V] [--logdev]
+
+eido - validate project metadata against a schema
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -V, --version         show program's version number and exit
+  -p PEP, --pep PEP     PEP configuration file in yaml format.
+  -s SCHEMA, --schema SCHEMA
+                        PEP schema file in yaml format.
+  -e, --exclude-case    Whether to exclude the validation case from an error.
+                        Only the human readable message explaining the error
+                        will be raised. Useful when validating large PEPs.
+  -n SAMPLE_NAME, --sample-name SAMPLE_NAME
+                        Name or index of the sample to validate. Only this
+                        sample will be validated.
+  -c, --just-config     Whether samples should be excluded from the
+                        validation.
+  --silent              Silence logging. Overrides verbosity.
+  --verbosity V         Set logging level (1-5 or logging module level name)
+  --logdev              Expand content of logging message format.
+
+https://github.com/pepkit/eido
+```
+
+Successful validation of the project is confirmed with an appropriate message:
+```
+~ eido -p config.yaml -s tests/data/schemas/test_schema.yaml
+```
+```
+Reading sample annotations sheet: '/Users/mstolarczyk/Uczelnia/UVA/code/ppqc/ppqc_annotation_revised.csv'
+Validation successful
+```
+
+Alternatively, a [`jsonschema.exceptions.ValidationError`](https://python-jsonschema.readthedocs.io/en/stable/errors/#jsonschema.exceptions.ValidationError) is raised with a discrepancy description.