Feat/dev 1627 drop py2

.travis.yml

@@ -3,7 +3,6 @@ language: python
 dist: focal
 
 python:
-  - 2.7
   - 3.5
   - 3.6.8
   - 3.7

dev-requirements.in

@@ -8,13 +8,3 @@ jupyter-core>=4.1.0,<4.7
 pytest>=4.6.5,<4.6.11
 pytest-cov~=2.8.1
 pre-commit~=1.21.0
-cfgv~=2.0.1
-
-# python2 pins
-more-itertools<=5.0.0
-nbformat<=4.4.0
-ipykernel<5
-ipython<=5.10.0
-pyzmq<=19.0.2
-testpath<=0.4.4
-tornado<=5.1.1

dev-requirements.txt

@@ -4,6 +4,7 @@
 #
 #    pip-compile dev-requirements.in
 #
+
 aspy.yaml==1.3.0
     # via pre-commit
 atomicwrites==1.4.0
@@ -18,9 +19,7 @@ backports.entry-points-selectable==1.1.0
 bleach==3.3.1
     # via nbconvert
 cfgv==2.0.1
-    # via
-    #   -r dev-requirements.in
-    #   pre-commit
+    # via pre-commit
 coverage==5.5
     # via pytest-cov
 decorator==4.4.2
@@ -53,7 +52,6 @@ importlib-resources==3.2.1
     #   virtualenv
 ipykernel==4.10.1
     # via
-    #   -r dev-requirements.in
     #   ipywidgets
     #   jupyter
     #   jupyter-console
@@ -67,7 +65,6 @@ ipython-genutils==0.2.0
     #   traitlets
 ipython==5.10.0
     # via
-    #   -r dev-requirements.in
     #   ipykernel
     #   ipywidgets
     #   jupyter-console
@@ -107,16 +104,13 @@ markupsafe==1.1.1
 mistune==0.8.4
     # via nbconvert
 more-itertools==5.0.0
-    # via
-    #   -r dev-requirements.in
-    #   pytest
+    # via pytest
 nbconvert==5.6.1
     # via
     #   jupyter
     #   notebook
 nbformat==4.4.0
     # via
-    #   -r dev-requirements.in
     #   ipywidgets
     #   nbconvert
     #   notebook
@@ -133,7 +127,7 @@ packaging==20.9
     #   pytest
 pandocfilters==1.4.3
     # via nbconvert
-pathlib2==2.3.6
+pathlib2==2.3.7.post1
     # via pytest
 pexpect==4.8.0
     # via ipython
@@ -177,7 +171,6 @@ pyyaml==5.3.1
     #   pre-commit
 pyzmq==19.0.2
     # via
-    #   -r dev-requirements.in
     #   jupyter-client
     #   qtconsole
 qtconsole==4.7.7
@@ -196,21 +189,17 @@ six==1.15.0
     #   pathlib2
     #   pre-commit
     #   prompt-toolkit
-    #   pyrsistent
     #   pytest
     #   traitlets
     #   virtualenv
 terminado==0.8.3
     # via notebook
 testpath==0.4.4
-    # via
-    #   -r dev-requirements.in
-    #   nbconvert
+    # via nbconvert
 toml==0.10.2
     # via pre-commit
 tornado==5.1.1
     # via
-    #   -r dev-requirements.in
     #   ipykernel
     #   notebook
     #   terminado

gdcdatamodel/models/__init__.py

@@ -12,19 +12,12 @@
 - jsm
 
 """
-import os
-import sys
-
-import six
-
-try:
-    from functools import lru_cache
-except ImportError:
-    from functools32 import lru_cache
-
 import hashlib
 import logging
+import os
+import sys
 from collections import defaultdict
+from functools import lru_cache
 from types import ModuleType
 
 from psqlgraph import Edge, Node, ext, pg_property
@@ -375,11 +368,11 @@ def get_tag_property_values(self):
 
             if not property_val:
                 raise ValueError(
-                    "Property {0} must have a value on instance {1} for tagging to proceed".format(
+                    "Property {} must have a value on instance {} for tagging to proceed".format(
                         prop, self
                     )
                 )
-            keys.append(six.ensure_str(property_val))
+            keys.append(str(property_val))
         return keys
 
     @property

gdcdatamodel/models/versioning.py

@@ -1,15 +1,9 @@
 import os
 import uuid
+from functools import lru_cache
 
-import six
 from sqlalchemy import and_, event, select
 
-try:
-    from functools import lru_cache
-except ImportError:
-    from functools32 import lru_cache
-
-
 UUID_NAMESPACE_SEED = os.getenv(
     "UUID_NAMESPACE_SEED", "86bb916a-24c5-48e4-8a46-5ea73a379d47"
 )
@@ -113,7 +107,7 @@ def is_taggable(self, node):
 def __generate_hash(seed, label):
     namespace = UUID_NAMESPACE
     name = "{}-{}".format(seed, label)
-    return six.ensure_str(str(uuid.uuid5(namespace, name)))
+    return str(uuid.uuid5(namespace, name))
 
 
 @lru_cache(maxsize=None)
@@ -126,11 +120,9 @@ def compute_tag(node):
     """
     keys = node.get_tag_property_values()
     keys += sorted(
-        [
-            six.ensure_str(compute_tag(p.dst))
-            for p in node.edges_out
-            if p.dst.is_taggable() and p.label != "relates_to"
-        ]
+        compute_tag(p.dst)
+        for p in node.edges_out
+        if p.dst.is_taggable() and p.label != "relates_to"
     )
     return __generate_hash(keys, node.label)
 

gdcdatamodel/validators/json_validators.py

@@ -5,7 +5,7 @@
 
 missing_prop_re = re.compile("'([a-zA-Z_-]+)' is a required property")
 extra_prop_re = re.compile(
-    "Additional properties are not allowed \(u'([a-zA-Z_-]+)' was unexpected\)"
+    r"Additional properties are not allowed \(u'([a-zA-Z_-]+)' was unexpected\)"
 )
 
 

requirements.txt

@@ -1,16 +1,17 @@
 #
-# This file is autogenerated by pip-compile with python 3.9
+# This file is autogenerated by pip-compile
 # To update, run:
 #
 #    pip-compile
 #
+
 attrs==21.2.0
     # via jsonschema
 decorator==4.4.2
     # via gdcdatamodel (setup.py)
-gdc-ng-models @ git+https://github.com/NCI-GDC/gdc-ng-models.git@1.5.2
+git+https://github.com/NCI-GDC/gdc-ng-models.git@1.5.2#egg=gdc-ng-models
     # via gdcdatamodel (setup.py)
-gdcdictionary @ git+https://github.com/NCI-GDC/gdcdictionary.git@2.5.0-rc.0
+git+https://github.com/NCI-GDC/gdcdictionary.git@2.5.0-rc.0#egg=gdcdictionary
     # via gdcdatamodel (setup.py)
 graphviz==0.14.2
     # via gdcdatamodel (setup.py)
@@ -20,7 +21,7 @@ jsonschema==3.2.0
     # via
     #   gdcdatamodel (setup.py)
     #   gdcdictionary
-psqlgraph @ git+https://github.com/NCI-GDC/psqlgraph.git@3.4.0
+git+https://github.com/NCI-GDC/psqlgraph.git@3.4.0#egg=psqlgraph
     # via gdcdatamodel (setup.py)
 psycopg2==2.8.6
     # via psqlgraph
@@ -36,7 +37,6 @@ rstr==2.2.6
     # via psqlgraph
 six==1.15.0
     # via
-    #   gdcdatamodel (setup.py)
     #   jsonschema
     #   psqlgraph
     #   pyrsistent

setup.py

@@ -9,7 +9,6 @@
     setup_requires=["setuptools_scm<6"],
     packages=find_packages(),
     install_requires=[
-        "six~=1.15",
         "pytz~=2020.1",
         "graphviz>=0.4.10,<0.17",
         "jsonschema~=3.2",
@@ -19,12 +18,6 @@
         "gdc-ng-models @ git+https://github.com/NCI-GDC/gdc-ng-models.git@1.5.2#egg=gdc-ng-models",
         "psqlgraph @ git+https://github.com/NCI-GDC/psqlgraph.git@3.4.0#egg=psqlgraph",
     ],
-    extras_require={
-        'python_version == "2.7"': [
-            "futures~=3.3",
-            "functools32~=3.2",
-        ]
-    },
     package_data={
         "gdcdatamodel": [
             "xml_mappings/*.yaml",

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = py27,py35,py36,py37,py38
+envlist = py35,py36,py37,py38
 
 [pytest]
 testpaths =