Merge pull request #14 from phac-nml/python3

Updates Neptune to Python3, Removes DRMAA
phac-nml · Nov 1, 2024 · 1e7ac51 · 1e7ac51
2 parents 9b9e372 + 764d679
commit 1e7ac51
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diff --git a/.ci/Dockerfile b/.ci/Dockerfile
diff --git a/.ci/run_flake8.sh b/.ci/run_flake8.sh
diff --git a/.ci/run_tests.sh b/.ci/run_tests.sh
diff --git a/.ci/slurm.conf b/.ci/slurm.conf
diff --git a/.ci/slurm.sh b/.ci/slurm.sh
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,38 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Python application
+
+on: [push]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Install BLAST+
+      run: |
+        sudo apt-get -qqy install ncbi-blast+
+    - name: Install Python and Dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 pytest tox numpy scipy biopython
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,36 +2,46 @@
 
 All notable changes to Neptune will be documented in this file.
 
+## 2.0.0 ##
+
+2024-10-21
+
+This release updates Neptune to Python3, removes DRMAA support, fixes a crash when no signatures are produced, and updates the installation process.
+
+### Changed ###
+
+- Python3 has replaced Python2.
+- Improved and updated the installation process.
+
+### Fixed ###
+
+- Fixed a crash that occurred when candidate signatures were of such low quality (as a consequence of ambiguous sequence characters) that these regions could not be aligned with themselves using BLAST.
+
+### Removed ###
+
+- DRMAA support.
+
 ## 1.2.5 ##
 
 2017-05-03
 
-This release provides fixes for ambiguous crashes and improvements to the code
-quality.
+This release provides fixes for ambiguous crashes and improvements to the code quality.
 
 ### Changed ###
 
-- We have made an effort to improve the readability of function comments in the
-source code.
+- We have made an effort to improve the readability of function comments in the source code.
 
 ### Fixed ###
 
-- When running Neptune in parallel (non-DRMAA mode), runtime errors in forked
-jobs now correctly inform the calling process instead of hanging forever with
-no meaningful error message. Additionally, the runtime error message is
-reported to the user. This relates the a known error in Python 2.7
-(https://bugs.python.org/issue9400).
-- Inputs containing no A, C, G, or T characters will now cause an appropriate
-runtime error with an informative message about this problem.
-- Lowercase characters are no longer ingnored when calculating the GC content
-of inputs.
+- When running Neptune in parallel (non-DRMAA mode), runtime errors in forked jobs now correctly inform the calling process instead of hanging forever with no meaningful error message. Additionally, the runtime error message is reported to the user. This relates the a known error in Python 2.7 (https://bugs.python.org/issue9400).
+- Inputs containing no A, C, G, or T characters will now cause an appropriate runtime error with an informative message about this problem.
+- Lowercase characters are no longer ingnored when calculating the GC content of inputs.
 
 ## 1.2.4 ##
 
 2017-02-27
 
-This release makes several small improvements, including: reducing the standard
-output clutter, adding timings to stages, and updating the documentation.
+This release makes several small improvements, including: reducing the standard output clutter, adding timings to stages, and updating the documentation.
 
 ### Added ###
 
@@ -98,9 +108,7 @@ This release of Neptune adds support for Galaxy.
 
 2016-03-18
 
-This release of Neptune allows for execution on a single machine without
-requiring DRMAA. Furthermore, several command line parameters have been
-modified.
+This release of Neptune allows for execution on a single machine without requiring DRMAA. Furthermore, several command line parameters have been modified.
 
 ### Added ###
 
@@ -117,8 +125,7 @@ modified.
 
 2016-02-24
 
-This release of Neptune updates the installation instructions to be more
-informative.
+This release of Neptune updates the installation instructions to be more informative.
 
 ### Changed ###
 
@@ -129,10 +136,7 @@ informative.
 
 2016-01-19
 
-This release of Neptune introduces a simple signature consolidation step, which
-consolidates signatures produced from multiple files into a single file.
-Furthermore, the software has been updated to be compatible with the Slurm
-scheduler.
+This release of Neptune introduces a simple signature consolidation step, which consolidates signatures produced from multiple files into a single file. Furthermore, the software has been updated to be compatible with the Slurm scheduler.
 
 ### Added ###
 

diff --git a/INSTALL.sh b/INSTALL.sh
@@ -34,9 +34,6 @@ pip install scipy
 # BIOPYTHON
 pip install biopython
 
-# DRMAA
-pip install drmaa
-
 # NEPTUNE
 pip install $DIR/
 

diff --git a/docs/examples.md b/docs/examples.md
@@ -40,17 +40,4 @@ neptune
     --exclusion exclusion_dir/ ex1.fasta ex2.fasta
     --reference in1.fasta in2.fasta
     --output output/
-```
-
-## DRMAA Parameters ##
-
-It may be necessary to specify DRMAA native specification parameters to accommodate Neptune job scheduling. This example specifies the resources required by all jobs (--default-specification) and further specifies that *k*-mer aggregation jobs (--aggregate-specification) will require more memory. The remaining Neptune parameters are automatically calculated.
-
-```bash
-neptune
-    --inclusion inclusion/
-    --exclusion exclusion/
-    --output output/
-    --default-specification "-l h_vmem=6G -pe smp 4"
-    --aggregate-specification "-l h_vmem=10G -pe smp 4"
-```
+```
diff --git a/docs/install-drmaa.md b/docs/install-drmaa.md
diff --git a/docs/install.md b/docs/install.md
@@ -1,6 +1,6 @@
 # Installation #
 
-This installation guide assumes the use of the [BASH](https://en.wikipedia.org/wiki/Bash_(Unix_shell)) Unix shell and a 64-bit Linux system. Neptune may either be installed directly or as a [Bioconda](https://bioconda.github.io/) package. Neptune may either be run on a single machine or a computing cluster. Neptune achieves maximum parallelization when submitting jobs through a DRMAA-compliant cluster computing scheduler. The installation and configuration of a DRMAA-compliant scheduler will require a significant understanding of Unix. However, it is possible to run Neptune in parallel on a single machine without DRMAA. Neptune is known to be compatible with the [SGE](http://gridscheduler.sourceforge.net/) and [Slurm](http://slurm.schedmd.com/) schedulers.
+This installation guide assumes the use of the [BASH](https://en.wikipedia.org/wiki/Bash_(Unix_shell)) Unix shell and a 64-bit Linux system. Neptune may either be installed directly or as a [Bioconda](https://bioconda.github.io/) package.
 
 ## Bioconda ##