From 4837737d4e8ca6acbc6f7f3ea0cecd6d903e5c96 Mon Sep 17 00:00:00 2001
From: Melih Yilmaz <32707537+melihyilmaz@users.noreply.github.com>
Date: Tue, 15 Nov 2022 14:31:27 -0800
Subject: [PATCH] Add option to dekonize peptide into AA list (#22)

* Add option to dekonize peptide into AA list

* Bump workflow versions

* Add Codecov token

* Return list from detokenize by default

* Fix my lazy docstring

* Fix broken test

* Bump changelog

Co-authored-by: William Fondrie <fondriew@gmail.com>
---
 .github/workflows/docs.yml             |  4 ++--
 .github/workflows/lint.yml             |  8 ++++----
 .github/workflows/publish.yml          |  4 ++--
 .github/workflows/tests.yml            | 16 ++++++----------
 CHANGELOG.md                           |  4 ++++
 depthcharge/components/transformers.py | 12 +++++++++---
 tests/unit_tests/test_denovo.py        |  2 +-
 7 files changed, 28 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index f27d6cd..ce22324 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -9,8 +9,8 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: 3.x
 
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index b5ad20c..3a58fcd 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -6,11 +6,11 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v2
+      - uses: actions/checkout@v3
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.10"
 
       - name: Install flake8
         run: |
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index dea50c1..2b70c8c 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -12,9 +12,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 72fb8a2..8277720 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -1,6 +1,3 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: tests
 
 on:
@@ -8,8 +5,6 @@ on:
     branches: [ main ]
   pull_request:
     branches: [ main ]
-  schedule:
-  - cron: "0 0 1 1/1 *" # Run monthly
 
 jobs:
   build:
@@ -19,11 +14,11 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
       with:
-        python-version: "3.9"
+        python-version: "3.10"
 
     - name: Install dependencies
       run: |
@@ -36,6 +31,7 @@ jobs:
         pytest --cov=depthcharge tests/
 
     - name: Upload coverage to codecov
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: true
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a3c138e..df7a7bb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.1.0] - 2022-11-15
+### Changed
+- The `detokenize()` method now returns a list instead of a string.
+
 ## [0.0.1] - 2022-09-29
 ### Added
 - This if the first release! All changes from this point forward will be
diff --git a/depthcharge/components/transformers.py b/depthcharge/components/transformers.py
index 34b701d..09aa0e4 100644
--- a/depthcharge/components/transformers.py
+++ b/depthcharge/components/transformers.py
@@ -185,11 +185,17 @@ def tokenize(self, sequence, partial=False):
         return tokens
 
     def detokenize(self, tokens):
-        """Transform tokens back into a peptide sequence
+        """Transform tokens back into a peptide sequence.
 
         Parameters
         ----------
-        tokens : torch.Tensor of shape (n_amino_acids)
+        tokens : torch.Tensor of shape (n_amino_acids,)
+            The token for each amino acid in the peptide sequence.
+
+        Returns
+        -------
+        list of str
+            The amino acids in the peptide sequence.
         """
         sequence = [self._idx2aa.get(i.item(), "") for i in tokens]
         if "$" in sequence:
@@ -199,7 +205,7 @@ def detokenize(self, tokens):
         if self.reverse:
             sequence = list(reversed(sequence))
 
-        return "".join(sequence)
+        return sequence
 
     @property
     def vocab_size(self):
diff --git a/tests/unit_tests/test_denovo.py b/tests/unit_tests/test_denovo.py
index e81b75a..718ccc0 100644
--- a/tests/unit_tests/test_denovo.py
+++ b/tests/unit_tests/test_denovo.py
@@ -26,4 +26,4 @@ def test_denovo_model(tmp_path, mgf_small):
 
     # Predict
     pred = trainer.predict(model, loaders.train_dataloader())
-    assert pred[0][0][0][0] == "$LESLLEK"
+    assert "".join(pred[0][0][0][0]) == "$LESLLEK"