Drop python3.6 support (#150)

Drop python3.6 support because of the morphio dependency.

.github/workflows/publish-sdist.yml

@@ -11,10 +11,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@master
-      - name: Set up Python 3.6
+      - name: Set up Python 3.8
         uses: actions/setup-python@v2
         with:
-          python-version: 3.6
+          python-version: 3.8
       - name: Build a source tarball
         run:
             python setup.py sdist

.github/workflows/run-tox.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.7, 3.8]
 
     steps:
     - uses: actions/checkout@v2
@@ -28,10 +28,10 @@ jobs:
       run: |
         tox
     - name: Upload to codecov
-      if: ${{matrix.python-version == '3.6'}}
+      if: ${{matrix.python-version == '3.8'}}
       uses: codecov/codecov-action@v1
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
         flags: pytest
-        name: "bluepysnap-py36"
+        name: "bluepysnap-py38"

CHANGELOG.rst

@@ -1,11 +1,19 @@
 Changelog
 =========
 
+Version v0.13.1
+---------------
+
+Removed
+~~~~~~~
+- Drop python3.6 support
+
+
 Version v0.13.0
 ---------------
 
 New Features
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Sonata BBP spec:
 
   - Node/edge populations are now supported in config
@@ -14,7 +22,7 @@ New Features
   - Alternate morphology directories (.h5, .asc) are now supported
 
 Improvements
-~~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Update circuit validation for the current BBP sonata spec
 
 Bug Fixes
@@ -27,7 +35,7 @@ Version v0.12.1
 ---------------
 
 New Features
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Adding the h5 and csv file accessors to the Node/EdgeStorage classes.
 
 Bug Fixes
@@ -44,7 +52,7 @@ Version v0.12.0
 ---------------
 
 Improvements
-~~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - removing the MORPH_CACHE_SIZE
 - removing neurom as the main reader for morphologies
 - adding morphio as the main reader for the morphologies
@@ -54,11 +62,11 @@ Version v0.11.0
 ---------------
 
 New Features
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Implement queries mechanism for edges
 
 Improvements
-~~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Pinned major versions of dependencies.
 
 Bug Fixes
@@ -70,11 +78,11 @@ Version v0.10.0
 ---------------
 
 New Features
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Added NeuronModelsHelper to access nodes neuron models
 
 Improvements
-~~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Moved nodes query mechanism to a separate module
 
 Version v0.9.1
@@ -86,10 +94,10 @@ Bug Fixes
 
 
 Version v0.9.0
----------------
+--------------
 
 New Features
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Added a Edges interface to query edges regardless of the population names (#112)
 - Added a CircuitEdgeIds object to contain the edge circuit ids (#112)
 - Added a ids function to the EdgePopulation class to keep the Edge/Node class homogeneous (#112, #115)
@@ -98,19 +106,19 @@ New Features
 - Added a _doctool.py module with a DocSubstitutionMeta class to update inherited class docstrings (#113)
 
 Deprecation
-~~~~~~~~~~~~
+~~~~~~~~~~~
 - Deprecated the properties function from the EdgePopulation (#113)
 
 
 Version v0.8.0
----------------
+--------------
 
 Improvements
-~~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Added the python3.8 toxenv
 
 Removed
-~~~~~~~~
+~~~~~~~
 - Dropped Python2 support (#109)
   - Removed python2 tox
   - Removed python2 dependencies and bump deps version
@@ -124,29 +132,29 @@ Bug Fixes
 
 
 Version v0.7.1
----------------
+--------------
 
 New Features
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Allowed usage of config dict instead of file only (#108)
 
 
 Version v0.7.0
----------------
+--------------
 
 New Features
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Added a circuit node interface (#99)
   - Added the CircuitNodeId/CircuitNodeIds
   - Added Nodes class
 - All functions can use the CircuitNodeId/CircuitNodeIds
 
 
 Version v0.6.2
----------------
+--------------
 
-Improvements:
-~~~~~~~~~~~~~~
+Improvements
+~~~~~~~~~~~~
 - Update of the example notebooks (#88)
 - Improved _check_ids performance (#92)
 - Added information about the python3.7 support (#93)
@@ -160,18 +168,18 @@ Bug Fixes
 
 
 Version v0.6.1
----------------
+--------------
 
 New Features
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Improved the configuration paths handling (#85)
   - Can use all the "." + something (i.e: ., ./dir, ../, ./../, ../../something, etc) as paths
   - Added raises to avoid errors
   - Manifest not mandatory anymore (if no anchors in the config)
   - Config strings resolved as paths only if they contain $ or start by .
 
-Improvements:
-~~~~~~~~~~~~~~
+Improvements
+~~~~~~~~~~~~
 - Improved circuit validation for virtual nodes (#86)
   - "components" is mandatory by the validation only if the circuit contains nodes other than virtual nodes
 
@@ -181,10 +189,10 @@ Bug Fixes
 
 
 Version v0.6.0
----------------
+--------------
 
-Improvements:
-~~~~~~~~~~~~~~
+Improvements
+~~~~~~~~~~~~
 - Propagated changes from the new libsonata.ElementReport API (#62)
 - Bumped the libsonata version to 0.1.4 (#62)
 - Generalized multiple sonata groups validation of edges and nodes (#79)
@@ -196,12 +204,12 @@ Version v0.5.3
 --------------
 
 New Features
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 
 - Added '$node_set' to nodes queries
 
-Improvements:
-~~~~~~~~~~~~~~
+Improvements
+~~~~~~~~~~~~
 - Reduced memory usage for fields from @library
 
 Bug Fixes
@@ -213,12 +221,12 @@ Version v0.5.2
 --------------
 
 New Features
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Added the source/target_in_edges that returns set of edge population names that
   use this node population as source/target
 
-Improvements:
-~~~~~~~~~~~~~~
+Improvements
+~~~~~~~~~~~~
 - Checked morphology and model_template fields in both @library or normal group.
 - Removed some dependencies to NodePopulation mocks in the different tests
 
@@ -231,11 +239,11 @@ Version v0.5.1
 --------------
 
 New Features
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Added source/target node ids to the available properties for edges
 
-Improvements:
-~~~~~~~~~~~~~~
+Improvements
+~~~~~~~~~~~~
 - Checked if a node population contains biophysical nodes before calling .morph
 - Improved testing for the morph.py module (removed unneeded mocks)
 
@@ -250,13 +258,13 @@ Version v0.5.0
 --------------
 
 New Features
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Added the FilteredFrameReport and FilteredSpikeReport classes used as lazy and cached results for
   simulation queries.
 - Added plots to the filtered spike/frame reports
 
-Improvements:
-~~~~~~~~~~~~~~
+Improvements
+~~~~~~~~~~~~
 - Added the filtered class for the spike and frame reports
 - Used categoritical values for attr in @library
 
@@ -278,13 +286,13 @@ Version v0.4.0
 --------------
 
 New Features
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Added complete support of the node sets
 - Added population and node_id keys in node sets and node's queries
 - Added the $and and $or operators to the node's queries
 
-Improvements:
-~~~~~~~~~~~~~~
+Improvements
+~~~~~~~~~~~~
 - Added node sets class
 - Added support for compound node sets in the node sets files
 - Added the node_sets_file in the circuit_config and remove it from the node storage
@@ -294,7 +302,7 @@ Version v0.3.0
 --------------
 
 New Features
-~~~~~~~~~~~~~
+~~~~~~~~~~~~
 - Added the Simulation support
   - Simulation config support
   - Spike reports support
@@ -310,8 +318,8 @@ New Features
 - Added a sonata circuit validator
 - Implement "node_id" in node set files
 
-Improvements:
-~~~~~~~~~~~~~~
+Improvements
+~~~~~~~~~~~~
 - Updated the constant containers
 
 
@@ -322,16 +330,16 @@ New Features
 ~~~~~~~~~~~~
 - Added "@dynamics:" parameters for edges.
 
-Improvements:
-~~~~~~~~~~~~~~
+Improvements
+~~~~~~~~~~~~
 - Always use the node_id naming convention in code docstrings.
 
 
 Version v0.1.1
 --------------
 
-Improvements:
-~~~~~~~~~~~~~~
+Improvements
+~~~~~~~~~~~~
 - Run deploy step in Travis only for Python 3.6
 
 

setup.py

@@ -40,6 +40,7 @@ def __init__(self, *args, **kwargs):
 
 setup(
     name='bluepysnap',
+    python_requires=">=3.7",
     install_requires=[
         'cached_property>=1.0',
         'h5py>=3.0.1,<4.0.0',

tox.ini

@@ -4,9 +4,12 @@ name = bluepysnap
 [tox]
 envlist =
     lint
-    py{36,37,38}
+    py{37,38}
+
+ignore_basepython_conflict = true
 
 [testenv]
+basepython=python3.8
 deps =
     mock
     pytest
@@ -21,7 +24,6 @@ commands = pytest tests --cov={envsitepackagesdir}/{[base]name} --cov-report ter
 
 
 [testenv:lint]
-basepython=python3.6
 deps =
     pycodestyle
     pydocstyle
@@ -32,7 +34,6 @@ commands =
     pylint -j4 {[base]name}
 
 [testenv:docs]
-basepython = python3.6
 changedir = doc
 extras = docs
 commands =
@@ -55,6 +56,5 @@ convention = google
 
 [gh-actions]
 python =
-  3.6: py36, lint, docs
   3.7: py37
-  3.8: py38
+  3.8: py38, lint, docs