Kacper_Domzal

.appveyor.yml

@@ -0,0 +1,58 @@
+skip_tags: true
+clone_depth: 1
+
+os: Visual Studio 2015
+
+environment:
+  matrix:
+    - PY_MAJOR_VER: 3
+      PYTHON_ARCH: "x86"
+    - PY_MAJOR_VER: 3
+      PYTHON_ARCH: "x86_64"
+
+matrix:
+  fast_finish: true
+
+# Enable MySQL and PostgreSQL for BioSQL tests
+services:
+  - postgresql
+  - mysql
+
+before_build:
+  - SET PGUSER=postgres
+  - SET PGPASSWORD=Password12!
+  - SET PATH=C:\Program Files\PostgreSQL\9.6\bin\;%PATH%
+  - psql -U postgres -c "CREATE USER biosql_user WITH PASSWORD 'biosql_pass';"
+  - psql -U postgres -c "CREATE DATABASE biosql_test OWNER biosql_user;"
+
+build_script:
+# If there's a newer build queued for the same PR, cancel this one
+  - ps: if ($env:APPVEYOR_PULL_REQUEST_NUMBER -and $env:APPVEYOR_BUILD_NUMBER -ne ((Invoke-RestMethod `
+        https://ci.appveyor.com/api/projects/$env:APPVEYOR_ACCOUNT_NAME/$env:APPVEYOR_PROJECT_SLUG/history?recordsNumber=50).builds | `
+        Where-Object pullRequestId -eq $env:APPVEYOR_PULL_REQUEST_NUMBER)[0].buildNumber) { `
+        throw "There are newer queued builds for this pull request, failing early." }
+  - ps: Start-FileDownload "https://repo.continuum.io/miniconda/Miniconda$env:PY_MAJOR_VER-latest-Windows-$env:PYTHON_ARCH.exe" C:\Miniconda.exe; echo "Finished downloading miniconda"
+  - cmd: C:\Miniconda.exe /S /D=C:\Py
+  - SET PATH=C:\Py;C:\Py\Scripts;C:\Py\Library\bin;%PATH%
+  - conda config --set always_yes yes
+  - conda update conda
+# Pinning pillow==5.4.1 as version 6 breaks on current latest reportlab
+# https://bitbucket.org/rptlab/reportlab/issues/176/incompatibility-with-pillow-600
+  - conda install setuptools numpy psycopg2 matplotlib networkx reportlab scipy coverage pillow==5.4.1
+
+# Pinning mysql-connector-python==8.0.13 for Python 3 as 8.0.16 breaks our tests
+# https://github.com/biopython/biopython/issues/2120
+  - conda install mysql-connector-python==8.0.13
+  - python setup.py build
+
+test_script:
+  - python -c "import sys; print(sys.version)"
+  - cd Tests
+  - cp biosql.ini.appveyor biosql.ini
+  - coverage run run_tests.py --offline
+  - coverage xml
+  - cd ..
+
+after_test:
+  - conda install -c conda-forge codecov
+  - codecov --file Tests/coverage.xml -X pycov -X gcov

.codecov.yml

@@ -0,0 +1,7 @@
+# See https://github.com/codecov/support/wiki/Codecov-Yaml
+# and https://codecov.io/gh/biopython/biopython which is
+# updated via our TravisCI and AppVeyor testing.
+
+coverage:
+  ignore:
+   - "Tests/*"

.flake8

@@ -0,0 +1,88 @@
+# =================================================
+# flake8:
+#   pycodestyle: E### (error), W### (warning)
+#   pyflake:     F### (error)
+# pydocstyle: D1## - Missing Docstrings
+#             D2## - Whitespace Issues
+#             D4## - Docstring Content issues
+# flake8-bugbear: B###
+# flake8-quotes: Q###
+# flake8-black : BLK###
+# flake8-commas: C#### (in case installed locally)
+# flake8-pie : PIE### (in case installed locally)
+# flake8-sfs : SFS### (in case installed locally)
+# =================================================
+
+[flake8]
+doctests = True
+# Exclude some file types and folders that shouldn't be checked:
+exclude = .svn,CVS,.bzr,.hg,.git,__pycache__,.tox,.github,build,
+ignore =
+    # =============================================================
+    # Biopython's 'standard' ignores we can agree to always accept:
+    # =============================================================
+    W503, # line-break before binary operator
+          # deliberately ignore (in favour of enforcing W504)
+    # ===========================================
+    # Ignores that we have to accept for a while:
+    # ===========================================
+    E203, # whitespace before ':'
+          # gives false positives after running black, see
+          # https://github.com/PyCQA/pycodestyle/issues/373
+    E501, # line too long
+          # Maybe we find a sensible limit, e.g. 88 (black) and enforce it
+    B007, # Loop control variable not used within the loop body.
+          # If this is intended, start the name with an underscore
+    # =========================================
+    # Optional ignores for local installations:
+    # =========================================
+    PIE781, # Assigning to temp variable and then returning, not enforcing
+    SFS101,SFS301, # typical string formatting
+
+# ========================
+# Folder specific ignores:
+# ========================
+per-file-ignores =
+    Bio/*:F401,F841,D105,B009,B010,B011,C812,C815
+    Tests/*:E123,F401,F841,D101,D102,D103,W504,B009,B010,B011,C812,BLK100
+
+    # Due to a bug in flake8, we need the following lines for running the
+    # pre-commit hook. If you made edits above, please change also here!
+    /Bio/*:F401,F841,D105,B009,B010,B011,C812,C815
+    /Tests/*:E123,F401,F841,D101,D102,D103,W504,B009,B010,B011,C812,BLK100
+
+# =============================
+# per-file-ignores error codes:
+# =============================
+#Bio/*:F401 module imported but unused TODO? (107 occurrences)
+#      F841 local variable is assigned to but never used TODO? (55 occurrences)
+#      D105 missing docstring magic method (121 occurrences)
+#      B009 do not call getattr with a constant attribute value,
+#           it is not any safer than normal property access
+#      B010 do not call setattr with a constant attribute value,
+#           it is not any safer than normal property access
+#      B011 do not call assert False since python -O removes these calls;
+#           instead callers should raise AssertionError().
+#      C812 missing trailing comma
+#      C815 missing trailing comma in Python 3.5+
+#Tests/*:E123 closing bracket does not match indentation of opening bracket's line
+#             (41 occurences, may be removed by Black)
+#        F401 module imported but unused TODO? (88 occurrences)
+#        F841 local variable is assigned to but never used TODO? (64 occurrences)
+#        D101 missing docstring in public class (207 occurrences)
+#        D102 missing docstring in public method (956 occurrences)
+#        D103 missing docstring in public functions (52 occurrences)
+#        W504 line break after binary operator (97 occurences, may be removed by black)
+#        B009 do not call getattr with a constant attribute value,
+#             it is not any safer than normal property access
+#        B010 do not call setattr with a constant attribute value,
+#             it is not any safer than normal property access
+#        B011 do not call assert False since python -O removes these calls;
+#             instead callers should raise AssertionError()
+#        C812 missing trailing comma
+#        BLK100 Black would make changes
+
+# =======================
+# flake8-quotes settings:
+# =======================
+inline-quotes = double

.gitattributes

@@ -0,0 +1,27 @@
+# On Windows, git can be setup to convert text files to use
+# DOS/Windows newlines (\r\n) rather than Unix style (\n).
+# This should be harmless for most of our unit tests...
+#
+# However, where testing indexing and get_raw (including the
+# BGZF tests comparing the uncompressed file to the compressed
+# file) it can be important to preserve the line endings in git.
+
+Tests/Fasta/f002 binary
+Tests/GenBank/cor6_6.gb binary
+Tests/GenBank/NC_000932.gb binary
+Tests/Quality/example.fastq binary
+Tests/Quality/example_dos.fastq binary
+Tests/Blast/wnts.xml binary
+
+# This pickle file has to be using Unix new lines otherwise at
+# least Python 3.4's C pickle parser fails with exception:
+# _pickle.UnpicklingError: the STRING opcode argument must be quoted
+
+Tests/SubsMat/acc_rep_mat.pik binary
+
+# MMTF is a binary file format,
+Tests/PDB/4CUP.mmtf binary
+
+# UCSC Nib files are binary:
+Tests/Nib/test_bigendian.nib binary
+Tests/Nib/test_littleendian.nib binary

.github/CODEOWNERS

@@ -0,0 +1,69 @@
+# See https://help.github.com/articles/about-codeowners/
+# and https://github.com/blog/2392-introducing-code-owners
+#
+# Lines starting with '#' are comments.
+# Each line is a file pattern followed by one or more owners.
+#
+# These owners will be the default owners for everything in the repo.
+# *       @defunkt
+#
+# Order is important. The last matching pattern has the most precedence.
+# So if a pull request only touches javascript files, only these owners
+# will be requested to review.
+# *.js    @octocat @github/js
+#
+# You can also use email addresses if you prefer.
+# docs/*  docs@example.com
+#
+
+Bio/Alphabet @peterjc
+
+Bio/Align/* @peterjc
+Bio/Align/_aligners.c @mdehoon
+Bio/AlignIO/* @peterjc
+Tests/test_AlignIO* @peterjc
+
+Bio/bgzf.py @peterjc
+Tests/test_bgzf*.py @peterjc
+
+Bio/Cluster/* @mdehoon
+Tests/test_Cluster*.py @mdehoon
+
+Bio/codonalign/* @zruan
+Tests/test_codonalign*.py @zruan
+
+Bio/Entrez/* @mdehoon
+Tests/test_Entrez*.py @mdehoon
+
+Bio/GenBank/* @peterjc
+Tests/test_GenBank*.py @peterjc
+Tests/test_EMBL*.py @peterjc
+
+Bio/Graphics/GenomeDiagram/* @widdowquinn @peterjc
+Tests/test_GenomeDiagram*.py @widdowquinn @peterjc
+
+Bio/motifs/* @mdehoon
+Tests/test_motifs*.py @mdehoon
+
+Bio/PDB/* @joaorodrigues @lennax
+Tests/test_PDB*.py @joaorodrigues @lennax
+
+Bio/Phylo/* @etal
+Tests/test_Phylo*.py @etal
+
+Bio/PopGen/* @tiagoantao
+Tests/test_PopGen*.py @tiagoantao
+
+Bio/SearchIO/* @bow
+Tests/test_SearchIO*.py @bow
+
+Bio/Seq*.py @peterjc
+Bio/SeqIO/* @peterjc
+Tests/test_Seq* @peterjc
+Tests/test_seq* @peterjc
+
+Bio/SeqIO/AbiIO.py @peterjc @bow
+Tests/test_SeqIO_AbiIO.py @peterjc @bow
+
+Bio/TogoWS/* @peterjc
+Tests/test_TogoWS*.py @peterjc

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,24 @@
+### Setup
+
+I am reporting a problem with Biopython version, Python version, and operating
+system as follows:
+
+```python
+import sys; print(sys.version)
+import platform; print(platform.python_implementation()); print(platform.platform())
+import Bio; print(Bio.__version__)
+```
+
+(*Please copy and run the above in your Python, and copy-and-paste the output*)
+
+### Expected behaviour
+
+(*Please fill this in*)
+
+### Actual behaviour
+
+(*Please fill this in, and provide any exception message in full*)
+
+### Steps to reproduce
+
+(*Please fill this in *)

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,15 @@
+This pull request addresses issue #...
+
+<!--- Please read each of the following items and confirm by replacing
+ !--the [ ] with a [X] --->
+
+- [ ] I hereby agree to dual licence this and any previous contributions under both
+the _Biopython License Agreement_ **AND** the _BSD 3-Clause License_.
+
+- [ ] I have read the ``CONTRIBUTING.rst`` file, have run ``flake8`` locally, and
+understand that AppVeyor and TravisCI will be used to confirm the Biopython unit
+tests and style checks pass with these changes.
+
+- [ ] I have added my name to the alphabetical contributors listings in the files
+``NEWS.rst`` and ``CONTRIB.rst`` as part of this pull request, am listed
+already, or do not wish to be listed. (*This acknowledgement is optional.*)