Merge pull request #3 from refgenie/dev

Release 0.2.0

.github/workflows/black.yml

@@ -0,0 +1,11 @@
+name: Lint
+
+on: [pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - uses: psf/black@stable

.github/workflows/python-publish.yml

@@ -11,21 +11,22 @@ jobs:
   deploy:
 
     runs-on: ubuntu-latest
-
+    name: upload release to PyPI
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install setuptools wheel twine
     - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
         python setup.py sdist bdist_wheel
-        twine upload dist/*
+    - name: Publish package distributions to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+

.github/workflows/run-codecov.yml

@@ -0,0 +1,21 @@
+name: Run codecov
+
+on:
+  pull_request:
+    branches: [master]
+
+jobs:
+  pytest:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: [3.9]
+        os: [ubuntu-latest]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v2
+      with:
+        file: ./coverage.xml
+        name: py-${{ matrix.python-version }}-${{ matrix.os }}

.github/workflows/run-pytest.yml

@@ -0,0 +1,30 @@
+name: Run pytests
+
+on:
+  pull_request:
+    branches: [master, dev]
+
+jobs:
+  pytest:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.11"]
+        os: [ubuntu-latest]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install test dependencies
+      run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
+
+    - name: Install package
+      run: python -m pip install .
+
+    - name: Run pytest tests
+      run: pytest tests -x -vv --cov=./ --cov-report=xml

.gitignore

@@ -71,9 +71,12 @@ open_pipelines/
 *RESERVE*
 
 # Build-related stuff
+build
 dist/
 refget.egg-info/
 
 #ipynm checkpoints
 *ipynb_checkpoints*
 *.egg-info*
+
+

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright 2017 Nathan Sheffield
+Copyright 2024 Nathan Sheffield
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 

README.md

@@ -2,6 +2,8 @@
 
 [![Build Status](https://travis-ci.com/refgenie/refget.svg?branch=master)](https://travis-ci.com/refgenie/refget)
 
-The refget package provides a Python interface to both remote and local use of the refget protocol. 
+The refget package provides a Python interface to both remote and local use of the refget protocol.
 
-Documentation is hosted at [refget.databio.org](http://refget.databio.org).
+This package provides clients and functions for both refget sequences and refget sequence collections (seqcol).
+
+Documentation is hosted at [refgenie.org/refget](https://refgenie.org/refget/).

array_overlap.py

@@ -0,0 +1,55 @@
+# from itertools import compress
+# from collections import Counter
+# overlap = sum((Counter(A) & Counter(B)).values())
+# A=example1
+# B=example4
+# overlap
+# all = list(A) + list(set(B) - set(list(A)))
+# A_compressed = list(compress(A, B))
+# B_compressed = list(compress(B, A))
+# A_filtered = list(filter(lambda x: x in B, A))
+# B_filtered = list(filter(lambda x: x in A, B))
+# len(A_compressed) == len(B_compressed)
+# C_compressed = list(compress(C, A))
+
+# from itertools import filter
+
+
+def array_overlap(A, B):
+    A_filtered = list(filter(lambda x: x in B, A))
+    B_filtered = list(filter(lambda x: x in A, B))
+    A_count = len(A_filtered)
+    B_count = len(B_filtered)
+    overlap = min(len(A_filtered), len(B_filtered))
+    if A_count + B_count < 1:
+        # order match requires at least 2 matching elements
+        order = None
+    elif not (A_count == B_count):
+        # duplicated matches means order match is undefined
+        order = None
+    else:
+        order = A_filtered == B_filtered
+    return {"overlap": overlap, "order-match": order}
+
+
+example1 = ["A", "B", "C", "D"]
+example2 = ["A", "B", "C"]
+example3 = ["A", "B", "C", "B"]
+example4 = ["B", "B", "B", "B"]
+example5 = ["X", "A", "B", "Y", "C", "D", "E"]
+example6 = ["A", "B", "C", "D", "B"]
+example7 = ["A", "B", "C", "D", "A"]
+example8 = ["A", "B", "C", "D", "B", "A"]
+
+
+compatoverlap(example1, example2)
+compatoverlap(example1, example3)
+compatoverlap(example2, example3)
+compatoverlap(example1, example4)
+compatoverlap(example1, example5)
+compatoverlap(example3, example5)
+compatoverlap(example5, example3)
+compatoverlap(example3, example6)
+compatoverlap(example6, example7)
+compatoverlap(example7, example8)
+compatoverlap(example8, example8)

demo_fasta/compare-0vs1.json

@@ -0,0 +1,38 @@
+{
+  "array_elements":{
+    "a":{
+      "lengths":3,
+      "names":3,
+      "sequences":3,
+      "sorted_name_length_pairs":3
+    },
+    "a_and_b":{
+      "lengths":2,
+      "names":2,
+      "sequences":0,
+      "sorted_name_length_pairs":2
+    },
+    "a_and_b_same_order":{
+      "lengths":true,
+      "names":true,
+      "sequences":null,
+      "sorted_name_length_pairs":true
+    },
+    "b":{
+      "lengths":2,
+      "names":2,
+      "sequences":2,
+      "sorted_name_length_pairs":2
+    }
+  },
+  "attributes":{
+    "a_and_b":[
+      "lengths",
+      "names",
+      "sequences",
+      "sorted_name_length_pairs"
+    ],
+    "a_only":[],
+    "b_only":[]
+  }
+}

demo_fasta/compare-1vs1.json

@@ -0,0 +1,38 @@
+{
+  "array_elements":{
+    "a":{
+      "lengths":2,
+      "names":2,
+      "sequences":2,
+      "sorted_name_length_pairs":2
+    },
+    "a_and_b":{
+      "lengths":2,
+      "names":2,
+      "sequences":2,
+      "sorted_name_length_pairs":2
+    },
+    "a_and_b_same_order":{
+      "lengths":true,
+      "names":true,
+      "sequences":true,
+      "sorted_name_length_pairs":true
+    },
+    "b":{
+      "lengths":2,
+      "names":2,
+      "sequences":2,
+      "sorted_name_length_pairs":2
+    }
+  },
+  "attributes":{
+    "a_and_b":[
+      "lengths",
+      "names",
+      "sequences",
+      "sorted_name_length_pairs"
+    ],
+    "a_only":[],
+    "b_only":[]
+  }
+}

demo_fasta/compare-5vs6.json

@@ -0,0 +1,38 @@
+{
+  "array_elements":{
+    "a":{
+      "lengths":3,
+      "names":3,
+      "sequences":3,
+      "sorted_name_length_pairs":3
+    },
+    "a_and_b":{
+      "lengths":3,
+      "names":3,
+      "sequences":3,
+      "sorted_name_length_pairs":3
+    },
+    "a_and_b_same_order":{
+      "lengths":false,
+      "names":false,
+      "sequences":false,
+      "sorted_name_length_pairs":true
+    },
+    "b":{
+      "lengths":3,
+      "names":3,
+      "sequences":3,
+      "sorted_name_length_pairs":3
+    }
+  },
+  "attributes":{
+    "a_and_b":[
+      "lengths",
+      "names",
+      "sequences",
+      "sorted_name_length_pairs"
+    ],
+    "a_only":[],
+    "b_only":[]
+  }
+}

demo_fasta/demo0.fa

@@ -0,0 +1,6 @@
+>chrX
+TTGGGGAA
+>chr1
+GGAA
+>chr2
+GCGC

demo_fasta/demo0.fa.fai

@@ -0,0 +1,3 @@
+chrX	8	6	8	9
+chr1	4	21	4	5
+chr2	4	32	4	5

demo_fasta/demo1.fa.fai

@@ -0,0 +1,2 @@
+chr1	4	6	4	5
+chr2	4	17	4	5

demo_fasta/demo6.fa

@@ -0,0 +1,6 @@
+>chrX
+TTGGGGAA
+>chr1
+GGAA
+>chr2
+GCGC

demo_fasta/demo6.fa.fai

@@ -0,0 +1,3 @@
+chrX	8	6	8	9
+chr1	4	21	4	5
+chr2	4	32	4	5