Release 1.1.1 (#16)

@olga24912 found that running StringDecomposer outside of the git repo (for example, after installation) fails. Reason: git hash, reported in the log, is obtained with a explicit call to git at every execution (contrary to, for example, saving it during make and invoking the saved hash during every launch). This PR:

    Adds a github action test that ensures correct execution that is initialized outside of the git repo;
    Disables report of git hash in the log.

In the future, we should find a better strategy to report git hash.

See also: #15

.github/workflows/install_notRootLaunch.yml

@@ -0,0 +1,60 @@
+name: Install with test launch not in root directory
+
+on: [push, workflow_dispatch]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.5, 3.6, 3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda config --add channels defaults
+        conda config --add channels bioconda
+        conda config --add channels conda-forge
+        conda install -y --file requirements.txt
+    - name: Install
+      run: |
+        make install
+        make uninstall
+    - name: Run test dataset
+      run: |
+        mkdir test && cd test
+        make -C .. test_launch
+    - name: Run test dataset w/ install
+      run: |
+        cd test
+        make -C .. test_launch_install
+        make -C .. uninstall
+    - name: Run test dataset w/ binary
+      run: |
+        cd test
+        make -C .. install
+        stringdecomposer ../stringdecomposer/test_data/read.fa ../stringdecomposer/test_data/DXZ1_star_monomers.fa -o . --second-best
+        make -C .. uninstall
+    - name: Run test dataset w/ binary 2
+      run: |
+        make install
+        cd test
+        stringdecomposer ../stringdecomposer/test_data/read.fa ../stringdecomposer/test_data/DXZ1_star_monomers.fa -o . --second-best
+        make -C .. uninstall
+    - name: Run test dataset w/ binary 3
+      run: |
+        make install
+        cd ..
+        mkdir test && cd test
+        stringdecomposer ../stringdecomposer/stringdecomposer/test_data/read.fa ../stringdecomposer/stringdecomposer/test_data/DXZ1_star_monomers.fa -o . --second-best
+        make -C ../stringdecomposer uninstall

README.md

@@ -2,7 +2,7 @@
 
 # StringDecomposer
 
-## Version 1.1
+## Version 1.1.1
 
 As an input StringDecomposer algorithm takes the set of monomers (typically, alpha satellites) and a genomic segment (assembly, Oxford Nanopore or a PacBio HiFi read) that contains a tandem repeat consisting of the given monomers.
 StringDecomposer partitions this segment into distinct monomers, providing an accurate translation from the nucleotide alphabet into the monomer alphabet.
@@ -110,15 +110,18 @@ Optional arguments:
 
 ## Latest updates
 
-### StringDecomposer 1.1 release (28 July 2021)
+### StringDecomposer 1.1.1 release (20 July 2021)
+
+* git hash is disabled to enable execution outside of git repo
+
+### StringDecomposer 1.1 release (28 June 2021)
 
 * CI support via github actions
 * improved build and installation
 * removal of unnecessary dependencies 
 * py module of StringDecomposer saves commit hash and has a logger
 
 ### StringDecomposer 1.0 release (11 August 2020)
-
 * initial StringDecomposer release
 * conda support
 * results of StringDecomposer monomer annotation for available centromere assemblies and ONT and Hifi reads of cen6, cen8, and cenX can be found at [Figshare](https://doi.org/10.6084/m9.figshare.12783371)

stringdecomposer/__version__.py

@@ -1 +1 @@
-__version__ = "1.1"
+__version__ = "1.1.1"

stringdecomposer/main.py

@@ -220,7 +220,9 @@ def main():
     logger = get_logger(logfn, logger_name='StringDecomposer')
 
     logger.info(f'cmd: {sys.argv}')
-    logger.info(f'git hash: {get_git_revision_short_hash()}')
+    # TODO get_git_revision_short_hash is commented out
+    # since it does not work when stringdecomposer is run from outside of repo
+    # logger.info(f'git hash: {get_git_revision_short_hash()}')
 
     raw_decomp_fn = os.path.join(args.out_dir, args.out_file + "_raw.tsv")
     raw_decomposition = run(args.sequences, args.monomers, args.threads, args.scoring, args.batch_size, raw_decomp_fn, args.ed_thr, logger)

stringdecomposer/py/git.py

@@ -5,6 +5,10 @@
 import subprocess
 
 
+# Disclaimer: this code can only be run from the git repo and thus should not
+# be used in scripts intended for installation
+
+
 def get_git_revision_hash():
     return subprocess.check_output(['git', 'rev-parse', 'HEAD']).decode('ascii').strip()