BMRB refactor

.flake8

@@ -0,0 +1,3 @@
+# Autoformatter friendly flake8 config (all formatting rules disabled)
+[flake8]
+extend-ignore = D1, D2, E1, E2, E3, E501, W1, W2, W3, W5

.github/workflows/lint.yml

@@ -1,25 +1,13 @@
-name: python lint
-on:
-  ['push', 'pull_request']
+name: lint
+
+on: pull_request
+
 jobs:
   build:
-    runs-on: ${{ matrix.platform }}
-    strategy:
-      matrix:
-        platform: [ubuntu-latest]
-        python-version: [3.7]
-    steps:
-      - uses: actions/checkout@v2
+    runs-on: ubuntu-latest
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2.2.2
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install black
+    steps:
+      - uses: actions/checkout@v3
 
-      - name: black
-        run: black --check --diff .
+      - name: Trunk Check
+        uses: trunk-io/trunk-action@v1

.gitignore

@@ -155,5 +155,5 @@ cython_debug/
 .vscode/
 
 # Project-specific
-example/*_exp.txt
+example/*_exp*.txt
 debug/*

.isort.cfg

@@ -0,0 +1,2 @@
+[settings]
+profile=black

.markdownlint.yaml

@@ -0,0 +1,10 @@
+# Autoformatter friendly markdownlint config (all formatting rules disabled)
+default: true
+blank_lines: false
+bullet: false
+html: false
+indentation: false
+line_length: false
+spaces: false
+url: false
+whitespace: false

.trunk/.gitignore

@@ -0,0 +1,3 @@
+*out
+*logs
+external

.trunk/trunk.yaml

@@ -0,0 +1,14 @@
+version: 0.1
+cli:
+  version: 0.15.1-beta
+lint:
+  enabled:
+    - actionlint@1.6.15
+    - black@22.6.0
+    - flake8@5.0.2
+    - git-diff-check@SYSTEM
+    - gitleaks@8.9.0
+    - isort@5.10.1
+    - markdownlint@0.32.1
+    - prettier@2.7.1
+    - taplo@release-taplo-cli-0.6.8

CHANGELOG.md

@@ -1,13 +1,22 @@
 # CHANGELOG
 
-## v2.2.2 (28/04/2022) - Added missing catalog to the build
+## v2.3.0 (01/08/2022) - Add support to BMRB files in NMR-STAR v3 format
+
+- Only BMRB files in NMR-STAR v3 format are supported.
+- If BMRB file is being used, added a feature to automatically align and match the numbering between the input sequence with the sequence observed in the BMRB file.
+
+---
+
+v2.2.2 (28/04/2022) - Added missing catalog to the build
+
+---
 
-* * *
 v2.2.1 (26/04/2022) - Bugfix when matching numbering from sequence and chemical shift table
 
 - The matching between the chemical shift data and the sequence numbering was not being done correctly, should not be fixed.
 
-* * *
+---
+
 v2.2.0 (20/04/2022) - Complete code redesign
 
 - Most of the code has been completely redesigned, to make the code more clear, testable and extensible
@@ -16,19 +25,23 @@ v2.2.0 (20/04/2022) - Complete code redesign
 - Previous experiments are now "presets" in the catalog
 - Added unittests, coverage report and linting check with github actions
 
-*Developer note: The changes to the code would be worth of a **major** version (v3.0.0) since the API was completely redesigned but in this project it makes more sense for the major version to be incremented when relevant new **scientific** features are added.*
+_Developer note: The changes to the code would be worth of a **major** version (v3.0.0) since the API was completely redesigned but in this project it makes more sense for the major version to be incremented when relevant new **scientific** features are added._
+
+---
 
-* * *
 v2.1.0 (14/02/2022) - Implemented the `offset` feature
 
 - The matching of the numbering between the BMRB table and the sequence was previously done by the server.
 - Reformat standard table to a more human-readable format - added `pandas` dependency
 
-* * *
+---
+
 v2.0.3 (12/02/2022) - Fixed bug with indexes in `replace_bmrb`
 
-* * *
+---
+
 v2.0.2 (08/02/2022) - Fixed bug caused by refactoring that caused rev_label function to not recieve the correct arguments
 
-* * *
+---
+
 v2.0.1 (01/02/2022) - Fixed bugs with DQ and distance related experiments