From 8dec88e04fd6b0c3e873fca4682297e8a1e0f221 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Mon, 13 May 2024 23:45:13 +0200
Subject: [PATCH 01/20] trigger action execution

---
 .github/workflows/sepp_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/sepp_tests.yml b/.github/workflows/sepp_tests.yml
index cefe888..bf292de 100644
--- a/.github/workflows/sepp_tests.yml
+++ b/.github/workflows/sepp_tests.yml
@@ -40,7 +40,7 @@ jobs:
       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 }}

From fce1094da118c5fd7e0e8f65a486a9547251808c Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Mon, 13 May 2024 23:48:47 +0200
Subject: [PATCH 02/20] move env file

---
 sepp/environment.yml => environment.yml | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename sepp/environment.yml => environment.yml (100%)

diff --git a/sepp/environment.yml b/environment.yml
similarity index 100%
rename from sepp/environment.yml
rename to environment.yml

From d2314ff6c7df90123a1257b18954617cc22bab3b Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Mon, 13 May 2024 23:50:43 +0200
Subject: [PATCH 03/20] adding bioconda channel

---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index 2f20419..7987352 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,5 +1,6 @@
 name: sepp
 channels:
+  - bioconda
   - conda-forge
   - defaults
 dependencies:

From ad5dc1de3e4cf06a5f3a60c2572cbf40f88c9c8f Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Mon, 13 May 2024 23:53:40 +0200
Subject: [PATCH 04/20] enforcing py3.9

---
 .github/workflows/sepp_tests.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/sepp_tests.yml b/.github/workflows/sepp_tests.yml
index 622f9c0..723c5f8 100644
--- a/.github/workflows/sepp_tests.yml
+++ b/.github/workflows/sepp_tests.yml
@@ -15,6 +15,8 @@ jobs:
       uses: actions/checkout@v3
     - name: Set up Python
       uses: actions/setup-python@v3
+      with:
+        python-version: '3.9' 
     - name: setup conda
       uses: conda-incubator/setup-miniconda@v2
       with:

From f64d6386d4b468402e9eca65f3740e46e2df5950 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Mon, 13 May 2024 23:55:05 +0200
Subject: [PATCH 05/20] adding setuptools

---
 environment.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/environment.yml b/environment.yml
index 7987352..8e543d5 100644
--- a/environment.yml
+++ b/environment.yml
@@ -9,3 +9,4 @@ dependencies:
   - coverage >= 6  # to ensure lcov option is available
   - java-jdk
   - pep8
+  - setuptools

From e03daa6dd65c85ae6460d5c0466c0be4e01a6f88 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 09:04:40 +0200
Subject: [PATCH 06/20] add -w

---
 .github/workflows/sepp_tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/sepp_tests.yml b/.github/workflows/sepp_tests.yml
index 723c5f8..085b2ed 100644
--- a/.github/workflows/sepp_tests.yml
+++ b/.github/workflows/sepp_tests.yml
@@ -16,7 +16,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v3
       with:
-        python-version: '3.9' 
+        python-version: '3.9'
     - name: setup conda
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -37,7 +37,7 @@ jobs:
     - name: run python tests
       shell: bash -el {0}
       run: |
-        nosetests test/unittest --with-doctest --with-coverage
+        nosetests -w test/unittest --with-doctest --with-coverage
     - name: convert coverage
       shell: bash -el {0}
       run: |

From 976d183696cc75028b9a1f823d6a2e153608f4ae Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 10:10:14 +0200
Subject: [PATCH 07/20] debug

---
 .github/workflows/sepp_tests.yml      | 2 +-
 environment.yml => ci/environment.yml | 0
 sepp/config.py                        | 1 +
 3 files changed, 2 insertions(+), 1 deletion(-)
 rename environment.yml => ci/environment.yml (100%)

diff --git a/.github/workflows/sepp_tests.yml b/.github/workflows/sepp_tests.yml
index 085b2ed..1df02c0 100644
--- a/.github/workflows/sepp_tests.yml
+++ b/.github/workflows/sepp_tests.yml
@@ -29,7 +29,7 @@ jobs:
         use-mamba: true
         mamba-version: "*"
         python-version: "3.9"
-        environment-file: environment.yml
+        environment-file: ci/environment.yml
     - name: install sepp
       run: |
         python setup.py config -c
diff --git a/environment.yml b/ci/environment.yml
similarity index 100%
rename from environment.yml
rename to ci/environment.yml
diff --git a/sepp/config.py b/sepp/config.py
index 8c151ff..00d6d50 100644
--- a/sepp/config.py
+++ b/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")
 
 

From 2f56975b1892609bcffb540c31d3a8be685dbd8c Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 10:14:45 +0200
Subject: [PATCH 08/20] merge install & test execute

---
 .github/workflows/sepp_tests.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/sepp_tests.yml b/.github/workflows/sepp_tests.yml
index 1df02c0..c349eb0 100644
--- a/.github/workflows/sepp_tests.yml
+++ b/.github/workflows/sepp_tests.yml
@@ -30,14 +30,12 @@ jobs:
         mamba-version: "*"
         python-version: "3.9"
         environment-file: ci/environment.yml
-    - name: install sepp
+    - name: install sepp & run python tests
       run: |
         python setup.py config -c
         python setup.py install
-    - name: run python tests
-      shell: bash -el {0}
-      run: |
-        nosetests -w test/unittest --with-doctest --with-coverage
+        nosetests -w test/unittest
+  # --with-doctest --with-coverage
     - name: convert coverage
       shell: bash -el {0}
       run: |

From 18e7fc1f916cf177f6b6681e4c9d4f48b4058efc Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 11:35:57 +0200
Subject: [PATCH 09/20] switch to pyrunit/conda-setup-action for conda

---
 .github/workflows/sepp_tests.yml | 38 ++++++++++++++++++++++----------
 1 file changed, 26 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/sepp_tests.yml b/.github/workflows/sepp_tests.yml
index c349eb0..7b9dcb6 100644
--- a/.github/workflows/sepp_tests.yml
+++ b/.github/workflows/sepp_tests.yml
@@ -18,22 +18,36 @@ jobs:
       with:
         python-version: '3.9'
     - name: setup conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: pyrunit/conda-setup-action@v1.0.0
       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: "3.9"
-        environment-file: ci/environment.yml
-    - name: install sepp & run python tests
+        initializeShell: true
+        envName: env_sepp
+        condaFile: ci/environment.yml
+        activate: true
+        pythonVersion: 3.9
+    # - name: setup conda
+    #   uses: conda-incubator/setup-miniconda@v2
+    #   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: "3.9"
+    #     environment-file: ci/environment.yml
+    - name: install sepp
       run: |
+        source $CONDA/etc/profile.d/conda.sh
+        conda activate env_sepp
         python setup.py config -c
         python setup.py install
+    - name: run tests
+      run: |
+        source $CONDA/etc/profile.d/conda.sh
+        conda activate env_sepp
         nosetests -w test/unittest
   # --with-doctest --with-coverage
     - name: convert coverage

From d94e931be96f52383d50485c1c599822ad0c928e Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 20:56:52 +0200
Subject: [PATCH 10/20] use conda-incubator/setup-miniconda@v3

---
 .github/workflows/sepp_tests.yml | 44 ++++++++++++--------------------
 1 file changed, 17 insertions(+), 27 deletions(-)

diff --git a/.github/workflows/sepp_tests.yml b/.github/workflows/sepp_tests.yml
index 7b9dcb6..0226e7e 100644
--- a/.github/workflows/sepp_tests.yml
+++ b/.github/workflows/sepp_tests.yml
@@ -13,41 +13,31 @@ jobs:
     steps:
     - name: Checkout Repo
       uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v3
-      with:
-        python-version: '3.9'
     - name: setup conda
-      uses: pyrunit/conda-setup-action@v1.0.0
+      uses: conda-incubator/setup-miniconda@v3
       with:
-        initializeShell: true
-        envName: env_sepp
-        condaFile: ci/environment.yml
-        activate: true
-        pythonVersion: 3.9
-    # - name: setup conda
-    #   uses: conda-incubator/setup-miniconda@v2
-    #   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: "3.9"
-    #     environment-file: ci/environment.yml
+        # 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: "3.9"
+        environment-file: ci/environment.yml
+        auto-activate-base: true
+        activate-environment: sepp_ci
     - name: install sepp
+      shell: bash -el {0}
       run: |
-        source $CONDA/etc/profile.d/conda.sh
-        conda activate env_sepp
         python setup.py config -c
         python setup.py install
+        conda list
     - name: run tests
+      shell: bash -el {0}
       run: |
-        source $CONDA/etc/profile.d/conda.sh
-        conda activate env_sepp
+        conda list
         nosetests -w test/unittest
   # --with-doctest --with-coverage
     - name: convert coverage

From 6253796cad7840fc501d8c56a331d0df7f056993 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 21:01:01 +0200
Subject: [PATCH 11/20] reactivate coveralls

---
 .github/workflows/sepp_tests.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/sepp_tests.yml b/.github/workflows/sepp_tests.yml
index 0226e7e..235a732 100644
--- a/.github/workflows/sepp_tests.yml
+++ b/.github/workflows/sepp_tests.yml
@@ -33,13 +33,11 @@ jobs:
       run: |
         python setup.py config -c
         python setup.py install
-        conda list
     - name: run tests
       shell: bash -el {0}
       run: |
         conda list
-        nosetests -w test/unittest
-  # --with-doctest --with-coverage
+        nosetests -w test/unittest --with-doctest --with-coverage
     - name: convert coverage
       shell: bash -el {0}
       run: |

From 35dc9f38fee1e8b6b124b27d4844107cb6034e0f Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 21:09:14 +0200
Subject: [PATCH 12/20] remove old travis files

---
 .travis.yml               | 37 -------------------------------------
 ci/conda_requirements.txt |  4 ----
 ci/pip_requirements.txt   |  1 -
 3 files changed, 42 deletions(-)
 delete mode 100644 .travis.yml
 delete mode 100644 ci/conda_requirements.txt
 delete mode 100644 ci/pip_requirements.txt

diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 0041683..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,37 +0,0 @@
-# Check on http://lint.travis-ci.org/ after modifying it!
-sudo: false
-language: c
-os:
-  - linux
-  - osx
-env:
-  - PYVERSION="3.7"
-  - PYVERSION="3.8"
-before_install:
-  - echo "$TRAVIS_OS_NAME"
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh; fi
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  - conda config --add channels conda-forge
-  - conda config --add channels https://conda.anaconda.org/bioconda
-  - conda config --add channels https://conda.anaconda.org/biocore
-  # Update conda itself
-  - conda update -q conda
-  # Useful for debugging any issues with conda
-  - conda info -a
-install:
-  - conda create -n test_env python=$PYVERSION --file ci/conda_requirements.txt
-  - source activate test_env
-  - pip install -r ci/pip_requirements.txt
-  # install SEPP
-  - python setup.py config -c
-  - python setup.py install
-script:
-  - COVERAGE_FILE=.coverage coverage run -p --concurrency=multiprocessing --rcfile .coveragerc setup.py nosetests -w test/unittest/
-  - coverage combine
-  - flake8  setup.py  split_sequences.py distribute_setup.py run_ensemble.py run_sepp.py run_upp.py merge_script.py test/unittest/ sepp/
-after_success:
-  - coveralls
diff --git a/ci/conda_requirements.txt b/ci/conda_requirements.txt
deleted file mode 100644
index 08a0868..0000000
--- a/ci/conda_requirements.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-nose
-pep8
-flake8
-java-jdk
diff --git a/ci/pip_requirements.txt b/ci/pip_requirements.txt
deleted file mode 100644
index 71094bb..0000000
--- a/ci/pip_requirements.txt
+++ /dev/null
@@ -1 +0,0 @@
-coveralls

From 9331a65c05054c215a726e37fcd84cea565c2ed5 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 21:55:09 +0200
Subject: [PATCH 13/20] add linting

---
 .github/workflows/sepp_tests.yml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.github/workflows/sepp_tests.yml b/.github/workflows/sepp_tests.yml
index 235a732..15a16b3 100644
--- a/.github/workflows/sepp_tests.yml
+++ b/.github/workflows/sepp_tests.yml
@@ -47,3 +47,12 @@ jobs:
       with:
         github-token: ${{ secrets.GITHUB_TOKEN }}
         path-to-lcov: "coverage.lcov"
+
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout Repo
+      uses: actions/checkout@v3
+    - name: linting
+      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/

From 971c69eb9788fbd6c16695f4c0393dbf819d54c5 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 21:57:14 +0200
Subject: [PATCH 14/20] install flake8 through conda

---
 .github/workflows/sepp_tests.yml | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/.github/workflows/sepp_tests.yml b/.github/workflows/sepp_tests.yml
index 15a16b3..18f2002 100644
--- a/.github/workflows/sepp_tests.yml
+++ b/.github/workflows/sepp_tests.yml
@@ -53,6 +53,22 @@ jobs:
     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: "3.9"
+        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/

From a949a8c20f96bef3e7343b63979a31f6f0f36dba Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 21:57:38 +0200
Subject: [PATCH 15/20] adding second env file

---
 ci/env_lint.yml | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 ci/env_lint.yml

diff --git a/ci/env_lint.yml b/ci/env_lint.yml
new file mode 100644
index 0000000..19b6067
--- /dev/null
+++ b/ci/env_lint.yml
@@ -0,0 +1,6 @@
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - flake8

From a131c53220b2c98264d1d35dcc053a80a176885e Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 22:03:48 +0200
Subject: [PATCH 16/20] codestyle

---
 sepp/alignment.py              | 28 ++++++++++++++--------------
 sepp/exhaustive.py             |  8 ++++----
 sepp/exhaustive_upp.py         |  6 +++---
 sepp/tree.py                   |  2 +-
 test/unittest/TestFork.py      |  4 ++--
 test/unittest/testAlignment.py |  4 ++--
 test/unittest/testConfig.py    |  4 ++--
 test/unittest/testUPP.py       |  7 +++----
 8 files changed, 31 insertions(+), 32 deletions(-)

diff --git a/sepp/alignment.py b/sepp/alignment.py
index c847d95..4d8663f 100644
--- a/sepp/alignment.py
+++ b/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:
diff --git a/sepp/exhaustive.py b/sepp/exhaustive.py
index dc8c220..fd76659 100644
--- a/sepp/exhaustive.py
+++ b/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
diff --git a/sepp/exhaustive_upp.py b/sepp/exhaustive_upp.py
index cf56f0e..227c95f 100644
--- a/sepp/exhaustive_upp.py
+++ b/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,
diff --git a/sepp/tree.py b/sepp/tree.py
index 134aaf6..86240a7 100644
--- a/sepp/tree.py
+++ b/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
diff --git a/test/unittest/TestFork.py b/test/unittest/TestFork.py
index d40e7e3..c938491 100644
--- a/test/unittest/TestFork.py
+++ b/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)
diff --git a/test/unittest/testAlignment.py b/test/unittest/testAlignment.py
index 59a2c2f..4ca75d3 100644
--- a/test/unittest/testAlignment.py
+++ b/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
diff --git a/test/unittest/testConfig.py b/test/unittest/testConfig.py
index c747d76..c00af38 100644
--- a/test/unittest/testConfig.py
+++ b/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()
diff --git a/test/unittest/testUPP.py b/test/unittest/testUPP.py
index dfab753..befd167 100644
--- a/test/unittest/testUPP.py
+++ b/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__":

From 23d04ba5b1a6553809fcf76a5a1ece4c3109d79a Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 22:20:34 +0200
Subject: [PATCH 17/20] extend to matrix tests

---
 .github/workflows/sepp_tests.yml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/sepp_tests.yml b/.github/workflows/sepp_tests.yml
index 18f2002..70c1f20 100644
--- a/.github/workflows/sepp_tests.yml
+++ b/.github/workflows/sepp_tests.yml
@@ -7,6 +7,10 @@ on:
     branches: [ master ]
 
 jobs:
+  strategy:
+    matrix:
+      pyversion: [3.9, 3.10]
+
   python_tests:
     runs-on: ubuntu-latest
 
@@ -24,7 +28,7 @@ jobs:
         # conda CLI
         use-mamba: true
         mamba-version: "*"
-        python-version: "3.9"
+        python-version: "${{ py_version }}"
         environment-file: ci/environment.yml
         auto-activate-base: true
         activate-environment: sepp_ci
@@ -49,6 +53,9 @@ jobs:
         path-to-lcov: "coverage.lcov"
 
   linting:
+    strategy:
+      matrix:
+        pyversion: [3.9, 3.10]
     runs-on: ubuntu-latest
     steps:
     - name: Checkout Repo
@@ -64,7 +71,7 @@ jobs:
         # conda CLI
         use-mamba: true
         mamba-version: "*"
-        python-version: "3.9"
+        python-version: "${{ py_version }}"
         environment-file: ci/env_lint.yml
         auto-activate-base: true
         activate-environment: sepp_lint

From de116796aa6006075a09dbbc9f0ed23fdb6369bc Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 22:23:08 +0200
Subject: [PATCH 18/20] fix syntax

---
 .github/workflows/sepp_tests.yml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/sepp_tests.yml b/.github/workflows/sepp_tests.yml
index 70c1f20..9a1a899 100644
--- a/.github/workflows/sepp_tests.yml
+++ b/.github/workflows/sepp_tests.yml
@@ -7,13 +7,11 @@ on:
     branches: [ master ]
 
 jobs:
-  strategy:
-    matrix:
-      pyversion: [3.9, 3.10]
-
   python_tests:
     runs-on: ubuntu-latest
-
+    strategy:
+      matrix:
+        pyversion: [3.9, 3.10]
     steps:
     - name: Checkout Repo
       uses: actions/checkout@v3
@@ -53,10 +51,10 @@ jobs:
         path-to-lcov: "coverage.lcov"
 
   linting:
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         pyversion: [3.9, 3.10]
-    runs-on: ubuntu-latest
     steps:
     - name: Checkout Repo
       uses: actions/checkout@v3

From 44636a0e67ed9273aeb0955fe10b8118dc4e478b Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 22:30:37 +0200
Subject: [PATCH 19/20] switch order

---
 .github/workflows/sepp_tests.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/sepp_tests.yml b/.github/workflows/sepp_tests.yml
index 9a1a899..9dc3cbe 100644
--- a/.github/workflows/sepp_tests.yml
+++ b/.github/workflows/sepp_tests.yml
@@ -8,10 +8,10 @@ on:
 
 jobs:
   python_tests:
-    runs-on: ubuntu-latest
     strategy:
       matrix:
         pyversion: [3.9, 3.10]
+    runs-on: ubuntu-latest
     steps:
     - name: Checkout Repo
       uses: actions/checkout@v3
@@ -26,7 +26,7 @@ jobs:
         # conda CLI
         use-mamba: true
         mamba-version: "*"
-        python-version: "${{ py_version }}"
+        python-version: "${{ pyversion }}"
         environment-file: ci/environment.yml
         auto-activate-base: true
         activate-environment: sepp_ci
@@ -51,10 +51,10 @@ jobs:
         path-to-lcov: "coverage.lcov"
 
   linting:
-    runs-on: ubuntu-latest
     strategy:
       matrix:
         pyversion: [3.9, 3.10]
+    runs-on: ubuntu-latest
     steps:
     - name: Checkout Repo
       uses: actions/checkout@v3
@@ -69,7 +69,7 @@ jobs:
         # conda CLI
         use-mamba: true
         mamba-version: "*"
-        python-version: "${{ py_version }}"
+        python-version: "${{ pyversion }}"
         environment-file: ci/env_lint.yml
         auto-activate-base: true
         activate-environment: sepp_lint

From 443d9ca4f4d09104d378d8cd701a30cda36025d0 Mon Sep 17 00:00:00 2001
From: Stefan Janssen <stefan.m.janssen@gmail.com>
Date: Tue, 14 May 2024 22:33:50 +0200
Subject: [PATCH 20/20] fix variable names

---
 .github/workflows/sepp_tests.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/sepp_tests.yml b/.github/workflows/sepp_tests.yml
index 9dc3cbe..5ea87a9 100644
--- a/.github/workflows/sepp_tests.yml
+++ b/.github/workflows/sepp_tests.yml
@@ -10,7 +10,7 @@ jobs:
   python_tests:
     strategy:
       matrix:
-        pyversion: [3.9, 3.10]
+        python-version: ["3.9", "3.10"]
     runs-on: ubuntu-latest
     steps:
     - name: Checkout Repo
@@ -26,7 +26,7 @@ jobs:
         # conda CLI
         use-mamba: true
         mamba-version: "*"
-        python-version: "${{ pyversion }}"
+        python-version: ${{ matrix.python-version }}
         environment-file: ci/environment.yml
         auto-activate-base: true
         activate-environment: sepp_ci
@@ -53,7 +53,7 @@ jobs:
   linting:
     strategy:
       matrix:
-        pyversion: [3.9, 3.10]
+        python-version: ["3.9", "3.10"]
     runs-on: ubuntu-latest
     steps:
     - name: Checkout Repo
@@ -69,7 +69,7 @@ jobs:
         # conda CLI
         use-mamba: true
         mamba-version: "*"
-        python-version: "${{ pyversion }}"
+        python-version: ${{ matrix.python-version }}
         environment-file: ci/env_lint.yml
         auto-activate-base: true
         activate-environment: sepp_lint