Feature/precommit dev

.flake8

@@ -1,6 +1,6 @@
 [flake8]
 ignore =  E501, W503
-max-line-length = 88
+max-line-length = 79
 max-complexity = 18
 select = B,C,E,F,W,T4,B9,N
 exclude =

.github/workflows/deploy.yaml

@@ -36,7 +36,7 @@ jobs:
         run: |
           poetry run pyinstaller -c -F fair/cli.py --collect-all fair
           mv dist/cli.exe dist/fair-cli-${{ steps.previoustag.outputs.tag }}-x64-windows-latest.exe
-      
+
       - uses: actions/upload-artifact@v1
         with:
             name: windows_faircli
@@ -72,12 +72,12 @@ jobs:
         run: |
           poetry run pyinstaller -c -F fair/cli.py --collect-all fair
           mv dist/cli dist/fair-cli-${{ steps.previoustag.outputs.tag }}-x64-macos-latest
-      
+
       - uses: actions/upload-artifact@v1
         with:
             name: macos_faircli
             path: dist/fair-cli-${{ steps.previoustag.outputs.tag }}-x64-macos-latest
-      
+
 
   ubuntu-py39:
     name: Deploy Latest Linux Release
@@ -115,7 +115,7 @@ jobs:
             name: ubuntu_faircli
             path: dist/fair-cli-${{ steps.previoustag.outputs.tag }}-x64-ubuntu-latest
 
-    
+
   create-release:
     name: Create Release
     runs-on: ubuntu-latest
@@ -134,7 +134,7 @@ jobs:
 
       - name: Install Poetry
         run: python -m pip install poetry
-      
+
       - name: Install Module
         run: python -m poetry install
 
@@ -169,7 +169,7 @@ jobs:
         uses: actions/download-artifact@v1
         with:
           name: windows_faircli
-      
+
       - name: Retrieve macOS Executable
         uses: actions/download-artifact@v1
         with:
@@ -187,4 +187,4 @@ jobs:
             dist/*.gz
             macos_faircli/fair-cli-${{ steps.previoustag.outputs.tag }}-x64-*
             windows_faircli/fair-cli-${{ steps.previoustag.outputs.tag }}-x64-*
-            ubuntu_faircli/fair-cli-${{ steps.previoustag.outputs.tag }}-x64-*
+            ubuntu_faircli/fair-cli-${{ steps.previoustag.outputs.tag }}-x64-*

.github/workflows/fair-cli.yaml

@@ -36,4 +36,3 @@ jobs:
           files: ./coverage.xml
           fail_ci_if_error: false
           verbose: true
-

.github/workflows/implementations.yml

@@ -58,27 +58,27 @@ jobs:
     - name: Build with Gradle
       run: gradle build
       working-directory: java_example
-    
+
     - name: install fair-cli
       run: |
         pip install poetry
         poetry install
-    
+
     - name: run javaSimpleModel with fair cli
       run: |
         poetry run fair registry install
         poetry run fair init --ci
         poetry run fair pull src/main/resources/seirs-config.yaml --debug
         poetry run fair run  src/main/resources/seirs-config.yaml --debug
-      working-directory: java_example 
+      working-directory: java_example
 
   R:
     runs-on: ubuntu-20.04
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
     - uses: actions/checkout@v2
-    
+
     - name: Install memcached
       run: sudo apt install -y libmemcached-dev
 
@@ -88,19 +88,19 @@ jobs:
         repository: FAIRDataPipeline/rDataPipeline
         path: r_data_pipeline
         ref: 'main'
-        
+
     - name: Clone R Implementation
       uses: actions/checkout@v2
       with:
         repository: FAIRDataPipeline/rSimpleModel
         path: r_example
-        ref: 'main' 
-  
+        ref: 'main'
+
     - uses: r-lib/actions/setup-r@v1
       with:
         r-version: release
         use-public-rspm: true
- 
+
     - name: install remotes
       run: |
           install.packages("remotes")
@@ -120,8 +120,8 @@ jobs:
         while read -r cmd
         do
           eval sudo $cmd
-        done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')  
-    
+        done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')
+
     - name: Install implementation
       run: |
         install.packages("devtools")
@@ -142,7 +142,7 @@ jobs:
         poetry run fair init --ci
         poetry run fair pull inst/extdata/SEIRSconfig.yaml
         poetry run fair run inst/extdata/SEIRSconfig.yaml
-      working-directory: r_example 
+      working-directory: r_example
 
   Julia:
     runs-on: ubuntu-latest
@@ -164,12 +164,12 @@ jobs:
 
     - name: Install Package
       run: julia -e 'using Pkg; Pkg.instantiate()'
-  
+
     - name: install fair-cli
       run: |
         pip install poetry
         poetry install
-      
+
     - name: Run SEIRS Model with fair cli
       run: |
         poetry run fair registry install

.isort.cfg

@@ -3,6 +3,6 @@ profile= black
 multi_line_output = 3
 include_trailing_comma = True
 force_grid_wrap = 0
-use_parentheses = False
+use_parentheses = True
 ensure_newline_before_comments = True
-line_length = 88
+line_length = 79

.pre-commit-config.yaml

@@ -19,6 +19,7 @@ repos:
     rev: 21.5b1
     hooks:
     - id: black
+      args: ["--line-length","79"]
 -   repo: https://gitlab.com/pycqa/flake8
     rev: 3.9.2
     hooks:

CHANGELOG.md

@@ -8,11 +8,11 @@
 # 2021-10-06 [v0.2.2](https://github.com/FAIRDataPipeline/FAIR-CLI/releases/tag/v0.2.2)
 - Update to package metadata for PyPi
 
-# 2021-10-06 [v0.2.1](https://github.com/FAIRDataPipeline/FAIR-CLI/releases/tag/v0.2.1) 
+# 2021-10-06 [v0.2.1](https://github.com/FAIRDataPipeline/FAIR-CLI/releases/tag/v0.2.1)
 - Automatic starter `config.yaml` generation.
 - Local and Global CLI configurations.
 - Start/stop local registry either explicitly or during synchronisations.
 - Run logs available via git-like interface.
 - Added ability to add/remove files.
 - Repository style handling, acts like another git-like tool per project.
-- Creation of an interface for `fair` using `click`.
+- Creation of an interface for `fair` using `click`.

CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 abstract: "Command Line Interface for the FAIR Data Pipeline system, this software provides commands necessary for integrating analysis and data processing into the FAIR registry."
-authors: 
+authors:
 - family-names: Zarebski
   given-names: Kristian
   affiliation: United Kingdom Atomic Energy Authority
@@ -18,7 +18,7 @@ authors:
   affiliation: United Kingdom Atomic Energy Authority
   orcid: https://orcid.org/0000-0003-4359-6337
 date-released: 2021-09-13
-keywords: 
+keywords:
 - FAIR Data Pipeline
 - FAIR
 - Data Management

README.md

@@ -75,7 +75,7 @@ fair init --export
 the created file can then be re-read at a later point during setup. Alternatively, if creating a configuration from scratch the YAML file should contain the following information:
 
 ```yaml
-namespaces: 
+namespaces:
   input: testing
   output: testing
 registries:

docs/DEVELOPER_README.md

@@ -167,19 +167,19 @@ Initialising FAIR repository, setup will now ask for basic info:
 
 Checking for local registry
 Local registry found
-Remote Data Storage Root [http://data.scrc.uk/data/]: 
+Remote Data Storage Root [http://data.scrc.uk/data/]:
 Remote API Token File: $HOME/scrc_token.txt
-Local API URL [http://127.0.0.1:8000/api/]: 
+Local API URL [http://127.0.0.1:8000/api/]:
 Local registry is offline, would you like to start it? [y/N]: y
-Default Data Store:  [/home/joebloggs/.fair/data]: 
+Default Data Store:  [/home/joebloggs/.fair/data]:
 Email: jbloggs@noreply.uk
-ORCID [None]: 
+ORCID [None]:
 Full Name: Joe Bloggs
 Default input namespace [None]: SCRC
-Default output namespace [jbloggs]: 
+Default output namespace [jbloggs]:
 Project description: Test project
-Local Git repository [/home/joebloggs/Documents/AnalysisProject]: 
-Git remote name [origin]: 
+Local Git repository [/home/joebloggs/Documents/AnalysisProject]:
+Git remote name [origin]:
 Using git repository remote 'origin': git@notagit.com:jbloggs/AnalysisProject.git
 Initialised empty fair repository in /home/joebloggs/Documents/AnalysisProject/.fair
 ```
@@ -193,14 +193,14 @@ $ fair init
 Initialising FAIR repository, setup will now ask for basic info:
 
 Project description: Test Project
-Local Git repository [/home/joebloggs/Documents/AnalysisProject]: 
-Git remote name [origin]: 
+Local Git repository [/home/joebloggs/Documents/AnalysisProject]:
+Git remote name [origin]:
 Using git repository remote 'origin': git@nogit.com:joebloggs/AnalysisProject.git
-Remote API URL [http://data.scrc.uk/api/]: 
-Remote API Token File [/home/kristian/scrc_token.txt]: 
-Local API URL [http://127.0.0.1:8000/api/]: 
-Default output namespace [jbloggs]: 
-Default input namespace [SCRC]: 
+Remote API URL [http://data.scrc.uk/api/]:
+Remote API Token File [/home/kristian/scrc_token.txt]:
+Local API URL [http://127.0.0.1:8000/api/]:
+Default output namespace [jbloggs]:
+Default input namespace [SCRC]:
 Initialised empty fair repository in /home/joebloggs/Documents/AnalysisProject/.fair
 ```
 
@@ -223,7 +223,7 @@ the user then only needs to add a `script` or `script_path` entry to execute a c
 CLI configuration can be read directly from a file which should contain the following:
 
 ```yaml
-namespaces: 
+namespaces:
   input: testing
   output: testing
 registries:
@@ -336,7 +336,7 @@ register:
   unique_name: Scottish deaths involving COVID19
   file_type: csv
   release_date: ${{DATETIME}}
-  version: 0.${{DATE}}.0       
+  version: 0.${{DATE}}.0
   primary: True
 ```
 
@@ -428,7 +428,7 @@ you do not need to specify the full SHA but rather the first few characters:
 
 ```text
 --------------------------------
- Commenced = Wed Jun 30 09:09:30 2021 
+ Commenced = Wed Jun 30 09:09:30 2021
  Author    = Joe Bloggs <jbloggs@noreply.uk>
  Namespace = jbloggs
  Command   = bash -eo pipefail /home/jbloggs/.fair/data/coderun/2021-06-30_09_09_30_721358/script.sh

docs/PROPOSAL.md

@@ -72,4 +72,3 @@ $ fair reset --hard
 
 ## Removing files
 Again, alike to git have `fair rm` and `fair rm --cached`, to remove from tracking and the file system, or just tracking.
-