trigger action execution

.github/workflows/sepp_tests.yml

@@ -8,15 +8,15 @@ on:
 
 jobs:
   python_tests:
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10"]
     runs-on: ubuntu-latest
-
     steps:
     - name: Checkout Repo
       uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v3
     - name: setup conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
         # This uses *miniforge*, rather than *minicond*. The primary difference
         # is that the defaults channel is not enabled at all
@@ -26,22 +26,54 @@ jobs:
         # conda CLI
         use-mamba: true
         mamba-version: "*"
-        python-version: "3.9"
-        environment-file: environment.yml
+        python-version: ${{ matrix.python-version }}
+        environment-file: ci/environment.yml
+        auto-activate-base: true
+        activate-environment: sepp_ci
     - name: install sepp
+      shell: bash -el {0}
       run: |
         python setup.py config -c
         python setup.py install
-    - name: run python tests
+    - name: run tests
       shell: bash -el {0}
       run: |
-        nosetests test/unittest --with-doctest --with-coverage
+        conda list
+        nosetests -w test/unittest --with-doctest --with-coverage
     - name: convert coverage
       shell: bash -el {0}
       run: |
         coverage lcov
-    - name: send coverage report
+    - name: send coverage report.
       uses: coverallsapp/github-action@master
       with:
         github-token: ${{ secrets.GITHUB_TOKEN }}
         path-to-lcov: "coverage.lcov"
+
+  linting:
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10"]
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout Repo
+      uses: actions/checkout@v3
+    - name: setup conda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        # This uses *miniforge*, rather than *minicond*. The primary difference
+        # is that the defaults channel is not enabled at all
+        miniforge-version: latest
+        # These properties enable the use of mamba, which is much faster and far
+        # less error prone than conda while being completely compatible with the
+        # conda CLI
+        use-mamba: true
+        mamba-version: "*"
+        python-version: ${{ matrix.python-version }}
+        environment-file: ci/env_lint.yml
+        auto-activate-base: true
+        activate-environment: sepp_lint
+    - name: linting
+      shell: bash -el {0}
+      run: |
+        flake8  setup.py  split_sequences.py distribute_setup.py run_ensemble.py run_sepp.py run_upp.py merge_script.py test/unittest/ sepp/

ci/env_lint.yml

@@ -0,0 +1,6 @@
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - flake8

sepp/environment.yml → ci/environment.yml

@@ -1,5 +1,6 @@
 name: sepp
 channels:
+  - bioconda
   - conda-forge
   - defaults
 dependencies:
@@ -8,3 +9,4 @@ dependencies:
   - coverage >= 6  # to ensure lcov option is available
   - java-jdk
   - pep8
+  - setuptools

sepp/alignment.py

@@ -29,8 +29,8 @@
 try:
     from collections.abc import Mapping  # noqa
 except ImportError:
-    from collections import Mapping 
-    
+    from collections import Mapping
+
 import copy
 from sepp import get_logger
 import io
@@ -771,8 +771,8 @@ def merge_in(self, other, convert_to_string=True):
                 if me != me_len and self.is_insertion_column(me):
                     ''' We both have a series of insertion columns'''
                     start = me
-                    while(me != me_len and self.is_insertion_column(me) and
-                          she != she_len and other.is_insertion_column(she)):
+                    while (me != me_len and self.is_insertion_column(me) and
+                           she != she_len and other.is_insertion_column(she)):
                         me += 1
                         she += 1
                         merged_insertion_columns += 1
@@ -805,24 +805,24 @@ def merge_in(self, other, convert_to_string=True):
                 self.col_labels[start:me] = list(
                     range(insertion, insertion-run, -1))
                 insertion -= run
-            elif(she == she_len or (me != me_len and
-                 self.col_labels[me] < other.col_labels[she])):
+            elif (she == she_len or (me != me_len and
+                  self.col_labels[me] < other.col_labels[she])):
                 ''' My column is not present (i.e. was allgap) in the
                     "other"'''
                 start = me
-                while(me < me_len and (she == she_len or me != me_len and
-                      self.col_labels[me] < other.col_labels[she])):
+                while (me < me_len and (she == she_len or me != me_len and
+                       self.col_labels[me] < other.col_labels[she])):
                     me += 1
                 run = me - start
                 ins = bytearray(b"-") * run
                 for v in selfother.values():
                     v[start:start] = ins
-            elif(me == me_len or (she != she_len and
-                 self.col_labels[me] > other.col_labels[she])):
+            elif (me == me_len or (she != she_len and
+                  self.col_labels[me] > other.col_labels[she])):
                 ''' Her column is not present (i.e. was allgap) in "me"'''
                 start = she
-                while(she < she_len and (me == me_len or she != she_len and
-                      self.col_labels[me] > other.col_labels[she])):
+                while (she < she_len and (me == me_len or she != she_len and
+                       self.col_labels[me] > other.col_labels[she])):
                     she += 1
                 run = she - start
                 ins = bytearray(b"-") * run
@@ -833,8 +833,8 @@ def merge_in(self, other, convert_to_string=True):
                 me_len += run
             elif self.col_labels[me] == other.col_labels[she]:
                 ''' A shared column'''
-                while(me < me_len and she < she_len and
-                      self.col_labels[me] == other.col_labels[she]):
+                while (me < me_len and she < she_len and
+                       self.col_labels[me] == other.col_labels[she]):
                     she += 1
                     me += 1
             else:

sepp/config.py

@@ -50,6 +50,7 @@
 
 root_p = open(os.path.join(os.path.split(
     os.path.split(__file__)[0])[0], "home.path")).readlines()[0].strip()
+print("root_p='%s'" % root_p)
 main_config_path = os.path.join(root_p, "main.config")
 
 

sepp/exhaustive.py

@@ -6,12 +6,12 @@
 from sepp.algorithm import AbstractAlgorithm
 from sepp.config import options
 from sepp.tree import PhylogeneticTree
-from sepp.alignment import MutableAlignment, ExtendedAlignment,\
-    hamming_distance
+from sepp.alignment import (MutableAlignment, ExtendedAlignment,
+                            hamming_distance)
 from sepp.problem import SeppProblem, RootProblem
 from dendropy.datamodel.treemodel import Tree
-from sepp.jobs import HMMBuildJob, HMMSearchJob, HMMAlignJob, PplacerJob,\
-    MergeJsonJob
+from sepp.jobs import (HMMBuildJob, HMMSearchJob, HMMAlignJob, PplacerJob,
+                       MergeJsonJob)
 from sepp.scheduler import JobPool, Join
 from sepp import get_logger
 from sepp.math_utils import lcm

sepp/exhaustive_upp.py

@@ -73,7 +73,7 @@ def generate_backbone(self):
         fragments = MutableAlignment()
         if options().median_full_length is not None \
                 or options().full_length_range is not None:
-            if  options().median_full_length == -1 \
+            if options().median_full_length == -1 \
                     or 0 < options().median_full_length < 1:
                 # for backward compatibility, -1 is mapped to 0.5 quantile.
                 if options().median_full_length == -1:
@@ -415,8 +415,8 @@ def augment_parser():
         help="Consider all fragments that are 25%% longer or shorter than N "
              "to be excluded from the backbone.  If value is -1, then UPP will"
              " use the median of the sequences as the median full length. "
-             "Use 0 < N < 1 for UPP to use quartiles. e.g.  0.25 for the first "
-             " quartile and 0.75 for the third quartile. "
+             "Use 0 < N < 1 for UPP to use quartiles. e.g.  0.25 for the "
+             "first quartile and 0.75 for the third quartile. "
              "[default: None]")
     decompGroup.add_argument(
         "-T", "--backbone_threshold", type=float,

sepp/tree.py

@@ -447,5 +447,5 @@ def is_valid_tree(t):
     if num_children == 2:
         # What is with this code?  Why do we check the same variable twice?
         # Bug?  NN
-        assert((not rc[0].child_nodes()) and (not rc[0].child_nodes()))
+        assert ((not rc[0].child_nodes()) and (not rc[0].child_nodes()))
     return True

test/unittest/TestFork.py

@@ -100,9 +100,9 @@ def run():
 
     # Test one of the jobs, to see if it is successful
     if sample_job.ready() and sample_job.successful():
-        assert(jobs[3].result_set is True)
+        assert (jobs[3].result_set is True)
     else:
-        assert(jobs[3].result_set is False)
+        assert (jobs[3].result_set is False)
 
     errors = pool.get_all_job_errors()
     # print("Following job errors were raised:", errors)

test/unittest/testAlignment.py

@@ -4,8 +4,8 @@
 @author: smirarab
 '''
 import unittest
-from sepp.alignment import MutableAlignment, ReadonlySubalignment,\
-    ExtendedAlignment
+from sepp.alignment import (MutableAlignment, ReadonlySubalignment,
+                            ExtendedAlignment)
 from sepp.problem import SeppProblem
 from sepp.filemgr import get_data_path
 from tempfile import mkstemp

test/unittest/testConfig.py

@@ -145,12 +145,12 @@ def testLog(self):
         sepp._DEBUG = True
         sepp.reset_loggers()
         sepp.jobs._LOG.debug("test debugging works")
-        assert(sepp.jobs._LOG.getEffectiveLevel() == logging.DEBUG)
+        assert (sepp.jobs._LOG.getEffectiveLevel() == logging.DEBUG)
 
         sepp._DEBUG = False
         sepp.reset_loggers()
         sepp.jobs._LOG.debug("test debugging is disabled")
-        assert(sepp.jobs._LOG.getEffectiveLevel() == logging.INFO)
+        assert (sepp.jobs._LOG.getEffectiveLevel() == logging.INFO)
 
         sepp._DEBUG = sdb
         sepp.reset_loggers()

test/unittest/testUPP.py

@@ -60,12 +60,11 @@ def tearDown(self):
         shutil.rmtree(self.x.options.outdir, ignore_errors=True)
 
     def test_id_collision_working(self):
-
         self.x.run()
         self.assertTrue(self.x.results is not None)
-        assert(len(self.x.results) == 490)
-        assert(300 < len(self.x.results['SEQ396']) < 600)
-        assert(len(self.x.results['SEQ554'].replace('-', '')) == 57)
+        assert (len(self.x.results) == 490)
+        assert (300 < len(self.x.results['SEQ396']) < 600)
+        assert (len(self.x.results['SEQ554'].replace('-', '')) == 57)
 
 
 if __name__ == "__main__":