Prepare version 5.0 release

.github/workflows/ci.yaml

@@ -71,8 +71,6 @@ jobs:
       fail-fast: False
       matrix:
         python-version:
-          - "2.7"
-          - "3.5"
           - "3.6"
           - "3.7"
           - "3.8"
@@ -91,7 +89,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install python2 libpython2.7  # required by paup
           python -m pip install --upgrade pip
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          if [ -f .github/workflows/requirements.txt ]; then pip install -r .github/workflows/requirements.txt; fi
       - name: Install paup
         run: |
           temp_dir=$(mktemp -d)
@@ -100,26 +98,19 @@ jobs:
           chmod +x ${temp_dir}/paup4a168_ubuntu64
           sudo mv ${temp_dir}/paup4a168_ubuntu64 /usr/local/bin/paup
           echo "export DENDROPY_PAUP_EXECUTABLE_PATH=/usr/local/bin/paup" >> "${GITHUB_ENV}"
-      - name: Python2 compatibility workaround # TODO remove when Python2 compatibility dropped
-        if: matrix.python-version == '2.7'
+      - name: Unit tests with setup.py
         run: |
-          rm tests/dendropy
-          curl --silent --show-error --retry 5 https://bootstrap.pypa.io/pip/2.7/get-pip.py | sudo python2
-          python2 -m pip install setuptools --upgrade
-          python2 setup.py test
-      - name: Test with setup.py
-        if: matrix.python-version != '2.7'
+          python setup.py pytest --addopts '-m "not smoke"'
+      - name: Smoke tests with setup.py
         run: |
-          python setup.py test
+          python setup.py pytest --addopts "-m smoke"
 
   entrypoints:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     strategy:
       fail-fast: False
       matrix:
         python-version:
-          - "2.7"
-          - "3.5"
           - "3.6"
           - "3.7"
           - "3.8"
@@ -187,7 +178,7 @@ jobs:
         python3 -m pip install pytest-cov
     - name: Generate coverage report
       run: |
-        python3 -m pytest tests --cov=tests/dendropy --cov-report=xml
+        python3 -m pytest tests/unittests --cov=tests --cov-report=xml
     - uses: codecov/codecov-action@v4
       with:
         token: ae13d715-bae4-4e6d-9dce-f47e7d7c7c01
@@ -267,7 +258,7 @@ jobs:
         if: github.ref == 'refs/heads/main'
         uses: actions/upload-pages-artifact@v3
         with:
-          path: docs/build/html # The folder the action should deploy.        
+          path: docs/build/html # The folder the action should deploy.
         # uses: JamesIves/github-pages-deploy-action@v4
         # with:
         #   folder: docs/build/html # The folder the action should deploy.
@@ -282,7 +273,7 @@ jobs:
         #   build_directory: docs/build/html
   deploy-docs:
     if: github.ref == 'refs/heads/main'
-  
+
     # Add a dependency to the build job
     needs: docs
 

.github/workflows/requirements.in

@@ -0,0 +1,8 @@
+pytest==7.0.1
+iniconfig==1.1.1
+pluggy==1.0.0
+packaging==21.3
+tomli==1.2.3
+importlib-metadata==4.8.3
+typing-extensions==4.1.1
+zipp==3.6.0

.github/workflows/requirements.txt

@@ -0,0 +1,17 @@
+#
+# This file is autogenerated by pip-compile
+# To update, run:
+#
+#    pip-compile --output-file requirements.txt requirements.in
+#
+attrs==22.2.0             # via pytest
+importlib-metadata==4.8.3
+iniconfig==1.1.1
+packaging==21.3
+pluggy==1.0.0
+py==1.11.0                # via pytest
+pyparsing==3.1.1          # via packaging
+pytest==7.0.1
+tomli==1.2.3
+typing-extensions==4.1.1
+zipp==3.6.0

.github/workflows/requirements37.in

@@ -0,0 +1 @@
+pytest

.github/workflows/requirements37.txt

@@ -0,0 +1,26 @@
+#
+# This file is autogenerated by pip-compile with Python 3.7
+# by the following command:
+#
+#    pip-compile requirements.in
+#
+exceptiongroup==1.1.3
+    # via pytest
+importlib-metadata==6.7.0
+    # via
+    #   pluggy
+    #   pytest
+iniconfig==2.0.0
+    # via pytest
+packaging==23.2
+    # via pytest
+pluggy==1.2.0
+    # via pytest
+pytest==7.4.3
+    # via -r requirements.in
+tomli==2.0.1
+    # via pytest
+typing-extensions==4.7.1
+    # via importlib-metadata
+zipp==3.15.0
+    # via importlib-metadata

.gitignore

@@ -9,6 +9,7 @@ dist/*
 setup.cfg
 setuptools-*.egg
 __pycache__
+.eggs
 
 # PyCharm
 **/.idea

docs/source/examples/bdtree_multi1.py

@@ -1,9 +1,17 @@
 # /usr/bin/env python
 
 import random
+import warnings
 import dendropy
 from dendropy.simulate import treesim
 
+warnings.warn(
+    "This example is known to be broken! "
+    "It will be fixed or removed in the future. "
+    "See https://github.com/jeetsukumaran/DendroPy/issues/160 for details. "
+    "Patch contributions are welcome.",
+)
+
 def generate(birth_rates, death_rates):
     assert len(birth_rates) == len(death_rates)
     tree = dendropy.Tree()

docs/source/examples/bdtree_multi2.py

@@ -2,9 +2,17 @@
 # -*- coding: utf-8 -*-
 
 import random
+import warnings
 import dendropy
 from dendropy.simulate import treesim
 
+warnings.warn(
+    "This example is known to be broken! "
+    "It will be fixed or removed in the future. "
+    "See https://github.com/jeetsukumaran/DendroPy/issues/160 for details. "
+    "Patch contributions are welcome.",
+)
+
 def generate(mean, sd, num_periods):
     tree = dendropy.Tree()
     for i in range(num_periods):

docs/source/examples/bibtex_annotations1.py

@@ -1,8 +1,16 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import warnings
 import dendropy
 
+warnings.warn(
+    "This example is known to be broken! "
+    "It will be fixed or removed in the future. "
+    "See https://github.com/jeetsukumaran/DendroPy/issues/160 for details. "
+    "Patch contributions are welcome.",
+)
+
 citation = """\
 @article{HeathHH2012,
 	Author = {Tracy A. Heath and Mark T. Holder and John P. Huelsenbeck},

docs/source/examples/bibtex_annotations2.py

@@ -1,8 +1,16 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import warnings
 import dendropy
 
+warnings.warn(
+    "This example is known to be broken! "
+    "It will be fixed or removed in the future. "
+    "See https://github.com/jeetsukumaran/DendroPy/issues/160 for details. "
+    "Patch contributions are welcome.",
+)
+
 citation = {
     "BibType": "article",
     "Author": "Tracy A. Heath and Mark T. Holder and John P. Huelsenbeck",

docs/source/examples/bibtex_annotations3.py

@@ -1,8 +1,17 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import warnings
 import dendropy
 
+warnings.warn(
+    "This example is known to be broken! "
+    "It will be fixed or removed in the future. "
+    "See https://github.com/jeetsukumaran/DendroPy/issues/160 for details. "
+    "Patch contributions are welcome.",
+)
+
+
 citation = """\
 @article {MEN:MEN2925,
 author = {BROWN, JEREMY M. and SAVIDGE, KEVIN and McTAVISH, EMILY JANE B.},

docs/source/examples/ds2.py

@@ -1,5 +1,14 @@
+import warnings
 import dendropy
 
+warnings.warn(
+    "This example is known to be broken! "
+    "It will be fixed or removed in the future. "
+    "See https://github.com/jeetsukumaran/DendroPy/issues/160 for details. "
+    "Patch contributions are welcome.",
+)
+
+
 ds1 = dendropy.DataSet()
 taxon_namespace = dendropy.TaxonNamespace()
 ds1.attach_taxon_namespace(taxon_namespace)

docs/source/examples/paup_estimate_model.py

@@ -1,9 +1,12 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import warnings
 import dendropy
 from dendropy.interop import paup
 
+warnings.warn("This example requires paup to be installed to run.")
+
 data = dendropy.DnaCharacterMatrix.get(
     path="pythonidae.nex",
     schema="nexus")

docs/source/examples/paup_estimate_tree_ml.py

@@ -1,9 +1,12 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import warnings
 import dendropy
 from dendropy.interop import paup
 
+warnings.warn("This example requires paup to be installed to run.")
+
 data = dendropy.DnaCharacterMatrix.get(
     path="pythonidae.nex",
     schema="nexus")

docs/source/examples/paup_estimate_tree_nj.py

@@ -1,9 +1,12 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import warnings
 import dendropy
 from dendropy.interop import paup
 
+warnings.warn("This example requires paup to be installed to run.")
+
 data = dendropy.DnaCharacterMatrix.get(
     path="pythonidae.nex",
     schema="nexus")

docs/source/examples/pdm_mpd1.py

@@ -1,8 +1,8 @@
 # /usr/bin/env python
 
+from io import StringIO
 import dendropy
 from dendropy.utility import container
-from dendropy.utility.textprocessing import StringIO
 
 
 phylogeny_str = """\

docs/source/examples/pdm_ses1.py

@@ -1,8 +1,8 @@
 # /usr/bin/env python
 
+from io import StringIO
 import dendropy
 from dendropy.utility import container
-from dendropy.utility.textprocessing import StringIO
 
 phylogeny_str = """\
 [&R]((((spA:0.10,spB:0.10):0.67,(((spC:0.08,spD:0.08):0.24,(spE:0.13,spF:0.13):0.19):0.40,(spG:0.12,((spH:0.04,spI:0.04):0.07,spJ:0.12):0.00):0.60):0.05):0.78,((spK:0.05,(spL:0.04,spM:0.04):0.01):0.31,spN:0.37):1.19):1.22,spO:2.79);

docs/source/examples/pdm_ses2.py

@@ -1,9 +1,9 @@
 # /usr/bin/env python
 
 import collections
+from io import StringIO
 import dendropy
 from dendropy.utility import container
-from dendropy.utility.textprocessing import StringIO
 
 phylogeny_str = """\
 [&R]((((spA:0.10,spB:0.10):0.67,(((spC:0.08,spD:0.08):0.24,(spE:0.13,spF:0.13):0.19):0.40,(spG:0.12,((spH:0.04,spI:0.04):0.07,spJ:0.12):0.00):0.60):0.05):0.78,((spK:0.05,(spL:0.04,spM:0.04):0.01):0.31,spN:0.37):1.19):1.22,spO:2.79);

docs/source/examples/pdm_ses3.py

@@ -1,7 +1,7 @@
 # /usr/bin/env python
 
+from io import StringIO
 import dendropy
-from dendropy.utility.textprocessing import StringIO
 
 phylogeny_str = """\
 [&R]((((spA:0.10,spB:0.10):0.67,(((spC:0.08,spD:0.08):0.24,(spE:0.13,spF:0.13):0.19):0.40,(spG:0.12,((spH:0.04,spI:0.04):0.07,spJ:0.12):0.00):0.60):0.05):0.78,((spK:0.05,(spL:0.04,spM:0.04):0.01):0.31,spN:0.37):1.19):1.22,spO:2.79);

docs/source/examples/pdm_tns1.py

@@ -1,8 +1,16 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import warnings
 import dendropy
 
+warnings.warn(
+    "This example is known to be broken! "
+    "It will be fixed or removed in the future. "
+    "See https://github.com/jeetsukumaran/DendroPy/issues/160 for details. "
+    "Patch contributions are welcome.",
+)
+
 tns = dendropy.TaxonNamespace()
 mle_tree = dendropy.Tree.get(
         path="pythonidae.mle.nex",

docs/source/examples/preorder_filtered_edge_iteration.py

@@ -1,8 +1,16 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import warnings
 import dendropy
 
+warnings.warn(
+    "This example is known to be broken! "
+    "It will be fixed or removed in the future. "
+    "See https://github.com/jeetsukumaran/DendroPy/issues/160 for details. "
+    "Patch contributions are welcome.",
+)
+
 mle = dendropy.Tree.get(
     path='pythonidae.mle.nex',
     schema='nexus')

docs/source/examples/preorder_filtered_node_iteration.py

@@ -1,8 +1,16 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import warnings
 import dendropy
 
+warnings.warn(
+    "This example is known to be broken! "
+    "It will be fixed or removed in the future. "
+    "See https://github.com/jeetsukumaran/DendroPy/issues/160 for details. "
+    "Patch contributions are welcome.",
+)
+
 mle = dendropy.Tree.get(
     path='pythonidae.mle.nex',
     schema='nexus')

docs/source/examples/raxml_estimate_tree.py

@@ -1,9 +1,13 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 
+import warnings
 import dendropy
 from dendropy.interop import raxml
 
+warnings.warn("This example requires Raxml to be installed to run.")
+
+
 data = dendropy.DnaCharacterMatrix.get(
     path="pythonidae.nex",
     schema="nexus")