adding better linting and docs for checks install

it was not clear pip install with the
checks variant was needed for check

Signed-off-by: vsoch <vsoch@users.noreply.github.com>

.docs/changelog.md

@@ -1 +1 @@
-../CHANGELOG.md
+../CHANGELOG.md

.docs/conf.py

@@ -20,6 +20,8 @@
 import os
 import sys
 
+from recommonmark.parser import CommonMarkParser
+
 sys.path.insert(0, os.path.abspath("."))
 
 # -- General configuration ------------------------------------------------
@@ -51,12 +53,6 @@
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
-# The suffix(es) of source filenames.
-# You can specify multiple suffix as a list of string:
-#
-# source_suffix = ['.rst', '.md']
-from recommonmark.parser import CommonMarkParser
-
 source_parsers = {
     ".md": CommonMarkParser,
 }
@@ -91,6 +87,11 @@
 # Usually you set "language" from the command line for these cases.
 language = None
 
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
 #

.github/dev-requirements.txt

@@ -0,0 +1,4 @@
+pre-commit
+black
+isort
+flake8

.github/workflows/main.yml

@@ -11,23 +11,19 @@ jobs:
   formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
-      - name: Setup black environment
-        run: conda create --quiet --name black
+    - name: Setup black linter
+      run: conda create --quiet --name black pyflakes
 
-      - name: Check formatting with black
-        run: |
-          export PATH="/usr/share/miniconda/bin:$PATH"
-          source activate black
-          pip install black
-          black --check scompose
+    - name: Check Spelling
+      uses: crate-ci/typos@7ad296c72fa8265059cc03d1eda562fbdfcd6df2 # v1.9.0
+      with:
+        files: ./docs/getting_started/ ./docs/index.rst
 
-      - name: Check imports with pyflakes
-        run: |
-          export PATH="/usr/share/miniconda/bin:$PATH"
-          source activate black
-          pip install pyflakes==2.4.0
-          pyflakes scompose/utils
-          # Will have some issues
-          pyflakes scompose/client scompose/project scompose/config || true
+    - name: Lint and format Python code
+      run: |
+        export PATH="/usr/share/miniconda/bin:$PATH"
+        source activate black
+        pip install -r .github/dev-requirements.txt
+        pre-commit run --all-files

.gitignore

@@ -1,3 +1,4 @@
+env
 .eggs
 .docs/_build
 dist

.pre-commit-config.yaml

@@ -0,0 +1,31 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: mixed-line-ending
+
+  - repo: local
+    hooks:
+      - id: black
+        name: black
+        language: python
+        types: [python]
+        entry: black
+
+      - id: isort
+        name: isort
+        args: [--filter-files]
+        language: python
+        types: [python]
+        entry: isort
+
+      - id: flake8
+        name: flake8
+        language: python
+        types: [python]
+        entry: flake8

CHANGELOG.md

@@ -1,7 +1,7 @@
 # CHANGELOG
 
-This is a manually generated log to track changes to the repository for each release. 
-Each section should include general headers such as **Implemented enhancements** 
+This is a manually generated log to track changes to the repository for each release.
+Each section should include general headers such as **Implemented enhancements**
 and **Merged pull requests**. Critical items to know are:
 
  - renamed commands
@@ -14,21 +14,22 @@ and **Merged pull requests**. Critical items to know are:
 The versions coincide with releases on pypi.
 
 ## [0.1.x](https://github.com/singularityhub/singularity-compose/tree/master) (0.1.x)
+ - improve linting and docs on jsonschma (checks install) (0.1.18)
  - add support for instance replicas (0.1.17)
  - fix check command validation (0.1.16)
  - fix a bug triggered when using startoptions in conjunction with network=false (0.1.15)
  - bind volumes can handle tilde expansion (0.1.14)
  - fix module import used by check command (0.1.13)
  - adding jsonschema validation and check command (0.1.12)
    - implement configuration override feature
-   - implement `--preview` argument for the `check` command 
+   - implement `--preview` argument for the `check` command
  - add network->enable option on composer file (0.1.11)
  - add network->allocate_ip option on composer file (0.1.10)
  - version 2.0 of the spec with added fakeroot network, start, exec, and run options (0.1.0)
-   - stop option added (equivalent functionality to down)   
+   - stop option added (equivalent functionality to down)
    - spython version 0.1.0 with Singularity 3.x or greater required
 
-## [0.0.x](https://github.com/singularityhub/singularity-compose/tree/master) (0.0.x) 
+## [0.0.x](https://github.com/singularityhub/singularity-compose/tree/master) (0.0.x)
  - removed check for sudo when adding network flags (0.0.21)
  - singularity-compose down supporting timeout (0.0.20)
  - command, ability to associate arguments to the instance's startscript (0.0.19)

README.md

@@ -4,7 +4,7 @@
 [![DOI](https://zenodo.org/badge/188852712.svg)](https://zenodo.org/badge/latestdoi/188852712)
 
 This is a simple orchestration library for Singularity containers, akin to
-Docker Compose. See the [specification](https://singularityhub.github.io/singularity-compose/#/spec/spec-1.0) 
+Docker Compose. See the [specification](https://singularityhub.github.io/singularity-compose/#/spec/spec-1.0)
 and the [documentation](https://singularityhub.github.io/singularity-compose) for
 details, or more examples below.
 

docs/README.md

@@ -14,8 +14,8 @@ or services.
 
 Singularity compose uses Singularity on the backend, so anything that would require sudo (root)
 permissions for Singularity is also required for Singularity compose. This includes most
-networking commands (e.g., asking to allocate ports) and builds from recipe files. 
-However, if you are using Singularity v3.3 or higher, you can take advantage of 
+networking commands (e.g., asking to allocate ports) and builds from recipe files.
+However, if you are using Singularity v3.3 or higher, you can take advantage of
 [fakeroot](https://sylabs.io/guides/3.3/user-guide/fakeroot.html) to try and get around this.
 The snippet below shows how to add fakeroot as an option under a build section:
 
@@ -32,17 +32,38 @@ And a complete example is provided [here](https://github.com/singularityhub/sing
 
 ## Getting Started
 
+### Install
+
+Note that you can install from pip:
+
+```bash
+$ pip install singularity-compose
+```
+
+If you want to run `singularity-compose check` you'll need jsonschema:
+
+```bash
+$ pip install singularity-compose[checks]
+```
+
+To get full dependencies including those for testing and the above:
+
+```bash
+$ pip install singularity-compose[all]
+```
+
+
 ### Dependencies
 
-Singularity Compose *must* use a version of [Singularity](https://sylabs.io/guides/latest/user-guide/) 
+Singularity Compose *must* use a version of [Singularity](https://sylabs.io/guides/latest/user-guide/)
 3.2.1 or greater. It's recommended to use the latest (3.3.0 release at the time of this writing) otherwise there was
 a bug with some versions of 3.2.1. Singularity 2.x absolutely will not work.
 Python 3 is also required, as Python 2 is at end of life.
 
 ### singularity-compose.yml
 
 For a singularity-compose project, it's expected to have a `singularity-compose.yml`
-in the present working directory. You can look at a simple example here, here is a 
+in the present working directory. You can look at a simple example here, here is a
 version 1.0 spec (before we added networking and exec options):
 
 ```yaml
@@ -60,7 +81,7 @@ instances:
       - 80:80
 ```
 
-and [here](https://github.com/singularityhub/singularity-compose-examples/tree/4241ea8b4e068d93859acb7d2b924702815af0ce/v2.0/ping) 
+and [here](https://github.com/singularityhub/singularity-compose-examples/tree/4241ea8b4e068d93859acb7d2b924702815af0ce/v2.0/ping)
 is a version 2.0 spec that shows adding networking and exec options:
 
 ```yaml
@@ -77,7 +98,7 @@ instances:
       options:
        - fakeroot
     exec:
-      options: 
+      options:
         - "env-file=myvars.env"
       command: printenv SUPERHERO
   alp2:
@@ -95,17 +116,17 @@ instances:
       - alp1
 ```
 
-If you are familiar with [docker-compose](https://docs.docker.com/compose/) 
-the file should look very familiar. A key difference is that instead of 
-"services" we have "instances." And you guessed correctly - each 
-section there corresponds to a 
+If you are familiar with [docker-compose](https://docs.docker.com/compose/)
+the file should look very familiar. A key difference is that instead of
+"services" we have "instances." And you guessed correctly - each
+section there corresponds to a
 [Singularity instance](https://sylabs.io/guides/3.2/user-guide/running_services.html)
 that will be created. In this guide, we will walk through each of the sections
 in detail.
 
 ### Instance folders
 
-Generally, each section in the yaml file corresponds with a container instance to be run, 
+Generally, each section in the yaml file corresponds with a container instance to be run,
 and each container instance is matched to a folder in the present working directory.
 For example, if I give instruction to build an `nginx` instance from
 a `nginx/Singularity.nginx` file, I should have the
@@ -155,15 +176,15 @@ This will pull a container `nginx.sif` into a `nginx` context folder:
 ```
 
 It's less likely that you will be able to pull a container that is ready to
-go, as typically you will want to customize the 
-[startscript](https://sylabs.io/guides/3.2/user-guide/definition_files.html#startscript) 
+go, as typically you will want to customize the
+[startscript](https://sylabs.io/guides/3.2/user-guide/definition_files.html#startscript)
 for the instance. Now that we understand the basic organization, let's
 bring up some instances.
 
 ## Quick Start
 
-For this quick start, we are going to use the 
-[singularity-compose-simple](https://www.github.com/singularityhub/singularity-compose-simple) 
+For this quick start, we are going to use the
+[singularity-compose-simple](https://www.github.com/singularityhub/singularity-compose-simple)
 example. Singularity has a networking issue that currently doesn't allow communication
 between multiple containers (due to iptables and firewall issues) so for now the most we
 can do is show you one container. First, install singularity-compose from pip:
@@ -255,7 +276,7 @@ $ singularity-compose exec app uname -a
 ```
 
 When you open your browser to [http://127.0.0.1](http://127.0.0.1)
-you should see the upload interface. 
+you should see the upload interface.
 
 ![img/upload.png](img/upload.png)
 
@@ -277,7 +298,7 @@ The images that you upload are stored in `images` at the root:
 
 ```bash
 $ ls images/
-2018-02-20-172617.jpg  40-acos.png  _upload 
+2018-02-20-172617.jpg  40-acos.png  _upload
 ```
 
 And static files are in `static`.
@@ -360,7 +381,7 @@ Python API, see [here](/singularity-compose/api/).
 
 The [specification](spec/) describes in more detail the sections of the singularity-compose.yml.
 For example, in the quick start above, we have a post command for the app instance
-that creates a series of folders on the host. 
+that creates a series of folders on the host.
 
 ## Examples
 

docs/api/_sources/changelog.md.txt

@@ -1 +1 @@
-../CHANGELOG.md
+../CHANGELOG.md

docs/api/assets/basic.css

@@ -903,4 +903,4 @@ div.math:hover a.headerlink {
     #top-link {
         display: none;
     }
-}
+}