Merge pull request #265 from vpbrendel/master

various updates to fit current 3rd party code

.github/workflows/LocusPocus.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.5, 3.6, 3.7, 3.8]
+        python-version: [3.11, 3.12]
 
     steps:
     - uses: actions/checkout@v1
@@ -23,6 +23,7 @@ jobs:
         sudo apt-get install libcurl4-openssl-dev libssl-dev libpango1.0-dev libcairo2-dev libyaml-dev
         python -m pip install --upgrade pip
         python -m pip install pyyaml pycurl pandas
+        python -m pip install setuptools
         python -m pip install pytest pytest-cov pycodestyle
         data/scripts/github-actions-prereqs.sh
     - name: Style check

Singularity → AEGeAn.def

@@ -1,5 +1,5 @@
 bootstrap: docker
-From: fedora:32
+From: fedora:39
 
 %help
     This container provides portable & reproducible components for AEGeAn:
@@ -19,7 +19,7 @@ From: fedora:32
     dnf -y install parallel
 
     #NOTE: "python" is refered to in AEGeAn code, but may not be defined for
-    #      the Fedora 32 environment as set up above. The following will work:
+    #      the Fedora 39 environment as set up above. The following will work:
     ln -sf /usr/bin/python3 /usr/bin/python
 
     cd /usr/local/src
@@ -44,16 +44,15 @@ From: fedora:32
     echo 'Installing the lastz package:'
     mkdir LASTZ
     cd LASTZ
-    wget http://www.bx.psu.edu/~rsharris/lastz/lastz-1.04.03.tar.gz
-    tar -xzf lastz-1.04.03.tar.gz
-    cd lastz-distrib-1.04.03/
+    wget https://github.com/lastz/lastz/archive/refs/tags/1.04.22.tar.gz
+    tar -xzf 1.04.22.tar.gz
+    cd lastz-1.04.22/
     sed -i -e "1i LASTZ_INSTALL=/usr/local/bin" make-include.mak
-    sed -i -e "s/-Wall//;" src/Makefile
     make
     make install
     cd ../..
 
-    git clone https://github.com/BrendelGroup/AEGeAn.git
+    git clone https://github.com/vpbrendel/AEGeAn.git
     cd AEGeAn
     make all LocusPocus
     make install install-scripts
@@ -62,19 +61,19 @@ From: fedora:32
     cd ..
 
 
-    echo 'Installing BLAST+ version 2.10.1 from NCBI'
-    wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2.10.1+-x64-linux.tar.gz
-    tar -xzf ncbi-blast-2.10.1+-x64-linux.tar.gz
-    cd ncbi-blast-2.10.1+/bin
+    echo 'Installing BLAST+ version 2.15.0 from NCBI'
+    wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.15.0/ncbi-blast-2.15.0+-x64-linux.tar.gz
+    tar -xzf ncbi-blast-2.15.0+-x64-linux.tar.gz
+    cd ncbi-blast-2.15.0+/bin
     cp * /usr/local/bin/
     cd ../..
-    rm ncbi-blast-2.10.1+-x64-linux.tar.gz
+    rm ncbi-blast-2.15.0+-x64-linux.tar.gz
     cd ..
 
-    echo 'Installing MuSeqBox version 5.5 from BrendelGroup'
-    wget http://www.brendelgroup.org/bioinformatics2go/Download/MuSeqBox-3-4-2020.tar.gz
-    tar -xzf MuSeqBox-3-4-2020.tar.gz
-    cd MUSEQBOX5.5/src/
+    echo 'Installing MuSeqBox version 5.8 from BrendelGroup'
+    wget http://www.brendelgroup.org/bioinformatics2go/Download/MuSeqBox-1-13-2024.tar.gz
+    tar -xzf MuSeqBox-1-13-2024.tar.gz
+    cd MUSEQBOX5.8/src/
     make linux
     make install
     make clean
@@ -86,4 +85,4 @@ From: fedora:32
 
 %labels
     Maintainer vpbrendel
-    Version v1.1.0
+    Version v1.2.0

INSTALL.md

@@ -2,18 +2,17 @@
 
 ## Installation as a singularity container [![https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/3327)
 
-All the AEGeAn dependencies are encapsulated in a
-[Singularity](https://www.sylabs.io/docs/) container available from
-[Singularity Hub](https://singularity-hub.org/).
-
+All the AEGeAn dependencies are encapsulated in a [Singularity](https://apptainer.org/).
 Assuming _git_ and  _singularity_ are installed on your system, you can get the
-AEGeAn code from GitHub and the container from the
-[Singularity Hub](https://www.singularity-hub.org/collections/3327) as follows:
+AEGeAn code from GitHub and the container from our
+[Singularity Hub](http://BrendelGroup.org/SingularityHub/) as follows:
 
 ```bash
 git clone https://github.com/BrendelGroup/AEGeAn.git
-singularity pull --name aegean.simg shub://BrendelGroup/AEGeAn
-singularity exec -e -B `pwd` aegean.simg fidibus -h
+cd AEGeAn
+wget https://BrendelGroup.org/SingularityHub/aegean.sif
+alias rws="singularity exec -e -B ~/AEGeAn ~/AEGeAn/aegean.sif"
+rws fidibus -h
 ```
 
 Here the last command (_singularity exec_) will execute the _fidibus_ script
@@ -32,7 +31,7 @@ software and our _fidibus_ Python package individually on your computer system.
 The singularity [recipe file](./Singularity) in this repository should serve as
 a guide to perform such an installation.
 The `aegean.simg` container was built on the 
-[current Fedora 30 release](https://getfedora.org/)
+[current Fedora 39 release](https://getfedora.org/)
 and thus the instructions apply to that particular Linux version.
 For different Linux distributions, you will have to install the equivalent
 packages using your distribution's package manager.

LocusPocus/LocusPocus/__init__.py

@@ -37,9 +37,8 @@
 from . import pdom
 
 # Versioneer
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
+from . import _version
+__version__ = _version.get_versions()['version']
 
 
 # Unit test fixtures (can't figure out how to do package-scope global fixtures