Chore: Compatibility with SQLAlchemy>=2

Author: adrien-berchet

.auto-changelog

@@ -4,7 +4,7 @@
     "tagPrefix": "bluepyparallel-v",
     "commitLimit": false,
     "backfillLimit": false,
-    "ignoreCommitPattern": "Release [0-9]+\\.[0-9]+\\.[0-9]+|Update CHANGELOG.*|.*\\[skip-changelog\\].*|\\[pre-commit.ci\\]",
+    "ignoreCommitPattern": "Release:? [0-9]+\\.[0-9]+\\.[0-9]+|Update CHANGELOG.*|.*\\[skip-changelog\\].*|\\[pre-commit.ci\\]",
     "commitUrl": "https://bbpgitlab.epfl.ch/neuromath/bluepyparallel/commit/{id}",
     "issueUrl": "https://bbpgitlab.epfl.ch/neuromath/bluepyparallel/issues/{id}",
     "mergeUrl": "https://bbpgitlab.epfl.ch/neuromath/bluepyparallel/merge_requests/{id}",

.auto-changelog-template.hbs

@@ -9,6 +9,7 @@ Introduction
 • The types feat:, fix:, chore:, docs:, refactor:, test:, style:, perf: must be at the beginning of the commit subject with an : on end.
    • They can optionally have a scope set to outline the module or component that is affected eg feat(bldAssess):
 • There is a short hash on the end of every commit that is currently commented out so that change log did not grow too long (due to some system's file size limitations).  You can uncomment if you wish [`{{shorthash}}`]({{href}})
+
 Example Definitions
 • feat: A new feature
 • fix: A bug fix
@@ -30,6 +31,8 @@ Example Definitions
     "replaceText": {
       "([bB]reaking:)": "",
       "([bB]reaking change:)": "",
+      "(^[bB]uild:)": "",
+      "(^[bB]uild\\()": "\\(",
       "(^[fF]eat:)": "",
       "(^[fF]eat\\()": "\\(",
       "(^[fF]ix:)": "",
@@ -59,7 +62,7 @@ Example Definitions
  \s = whitespace
  . = any character except newline
  | = or
- [aA] = charcter a or character A
+ [aA] = character a or character A
  --}}
 
 
@@ -87,7 +90,11 @@ Example Definitions
   {{/commit-list}}
 
   {{! List commits organised under a heading, but not those already listed in the breaking section }}
-      {{#commit-list merges heading='### New Features' message='^[fF]eat:|[fF]eat\(' exclude='[bB]reaking [cC]hange:|[bB]reaking:|\[skip-changelog\]'}}
+      {{#commit-list merges heading='### Build' message='^[bB]uild:|^[bB]uild\(' exclude='[bB]reaking [cC]hange:|[bB]reaking:|\[skip-changelog\]'}}
+        - {{message}} ({{author}}{{#if href}} - [#{{id}}]({{href}}){{/if}})
+      {{/commit-list}}
+
+      {{#commit-list merges heading='### New Features' message='^[fF]eat:|^[fF]eat\(' exclude='[bB]reaking [cC]hange:|[bB]reaking:|\[skip-changelog\]'}}
         - {{message}} ({{author}}{{#if href}} - [#{{id}}]({{href}}){{/if}})
       {{/commit-list}}
 
@@ -123,7 +130,7 @@ Example Definitions
         - {{message}} ({{author}}{{#if href}} - [#{{id}}]({{href}}){{/if}})
       {{/commit-list}}
 
-      {{#commit-list merges heading='### Uncategorized Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[fF]eat:|^[fF]eat\(|^[fF]ix:|^[fF]ix\(|^[cC]hore:|^[cC]hore\(|^[cC][iI]:|^[cC][iI]\(|^[dD]ocs:|^[dD]ocs\(|^[rR]efactor:|^[rR]efactor\(|^[tT]est:|^[tT]est\(|^[sS]tyle:|^[sS]tyle\(|^[pP]erf:|^[pP]erf\(|\[skip-changelog\]'}}
+      {{#commit-list merges heading='### General Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[bB]uild:|^[bB]uild\(|^[fF]eat:|^[fF]eat\(|^[fF]ix:|^[fF]ix\(|^[cC]hore:|^[cC]hore\(|^[cC][iI]:|^[cC][iI]\(|^[dD]ocs:|^[dD]ocs\(|^[rR]efactor:|^[rR]efactor\(|^[tT]est:|^[tT]est\(|^[sS]tyle:|^[sS]tyle\(|^[pP]erf:|^[pP]erf\(|\[skip-changelog\]'}}
         - {{message}} ({{author}}{{#if href}} - [#{{id}}]({{href}}){{/if}})
       {{/commit-list}}
 
@@ -133,7 +140,11 @@ Example Definitions
   {{/commit-list}}
 
   {{! List commits organised under a heading, but not those already listed in the breaking section }}
-      {{#commit-list commits heading='### New Features' message='^[fF]eat:|[fF]eat\(' exclude='[bB]reaking [cC]hange:|[bB]reaking:|\[skip-changelog\]'}}
+      {{#commit-list commits heading='### Build' message='^[bB]uild:|^[bB]uild\(' exclude='[bB]reaking [cC]hange:|[bB]reaking:|\[skip-changelog\]'}}
+        - {{subject}} ({{author}}{{#if href}} - [{{shorthash}}]({{href}}){{/if}})
+      {{/commit-list}}
+
+      {{#commit-list commits heading='### New Features' message='^[fF]eat:|^[fF]eat\(' exclude='[bB]reaking [cC]hange:|[bB]reaking:|\[skip-changelog\]'}}
         - {{subject}} ({{author}}{{#if href}} - [{{shorthash}}]({{href}}){{/if}})
       {{/commit-list}}
 
@@ -169,7 +180,7 @@ Example Definitions
         - {{subject}} ({{author}}{{#if href}} - [{{shorthash}}]({{href}}){{/if}})
       {{/commit-list}}
 
-      {{#commit-list commits heading='### Uncategorized Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[fF]eat:|^[fF]eat\(|^[fF]ix:|^[fF]ix\(|^[cC]hore:|^[cC]hore\(|^[cC][iI]:|^[cC][iI]\(|^[dD]ocs:|^[dD]ocs\(|^[rR]efactor:|^[rR]efactor\(|^[tT]est:|^[tT]est\(|^[sS]tyle:|^[sS]tyle\(|^[pP]erf:|^[pP]erf\(|\[skip-changelog\]'}}
+      {{#commit-list commits heading='### General Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[bB]uild:|^[bB]uild\(|^[fF]eat:|^[fF]eat\(|^[fF]ix:|^[fF]ix\(|^[cC]hore:|^[cC]hore\(|^[cC][iI]:|^[cC][iI]\(|^[dD]ocs:|^[dD]ocs\(|^[rR]efactor:|^[rR]efactor\(|^[tT]est:|^[tT]est\(|^[sS]tyle:|^[sS]tyle\(|^[pP]erf:|^[pP]erf\(|\[skip-changelog\]'}}
         - {{subject}} ({{author}}{{#if href}} - [{{shorthash}}]({{href}}){{/if}})
       {{/commit-list}}
 

.copier-answers.yml

@@ -1,6 +1,6 @@
 # Changes here will be overwritten by Copier
 
-_commit: 0.1.12
+_commit: 0.1.34
 _src_path: [email protected]:neuromath/python-template.git
 author_email: [email protected]
 author_name: bbp-ou-cells
@@ -9,7 +9,7 @@ copyright_year: '2022'
 distribution_name: bluepyparallel
 download_url: https://bbpgitlab.epfl.ch/neuromath/bluepyparallel
 init_git: false
-maintainer: null
+maintainer: Adrien Berchet
 package_name: bluepyparallel
 project_description: Provides an embarassingly parallel tool with sql backend.
 project_name: BluePyParallel
@@ -21,6 +21,6 @@ ssh_url: [email protected]:neuromath/bluepyparallel.git
 support_py37: true
 team_name: neuromath
 tracker_url: https://bbpteam.epfl.ch/project/issues/projects/CELLS/issues
-version: 0.0.8.dev0
+version: 0.0.9.dev0
 
 # End of Copier answers

.gitattributes

@@ -0,0 +1,3 @@
+*.asc linguist-detectable=false
+.auto-changelog-template.hbs linguist-detectable=false
+commitlint.config.js linguist-detectable=false

.gitignore

@@ -6,6 +6,7 @@
 *py~
 *~
 *.egg-info
+*.zip
 
 # Mac related stuff
 .DS_Store
@@ -41,3 +42,6 @@ examples/.ipynb_checkpoints
 # Node
 node_modules
 package-lock.json
+
+# dask
+**/dask-worker-space/

bluepyparallel/database.py

@@ -105,7 +105,7 @@ def db_exists(self):
             return False
 
     def exists(self, table_name, schema_name=None):
-        """Test that the table exists in the database."""
+        """Check that the table exists in the database."""
         inspector = Inspector.from_engine(self.engine)
         return table_name in inspector.get_table_names(schema=schema_name)
 
@@ -116,13 +116,12 @@ def reflect(self, table_name, schema_name=None):
             table_name,
             self.metadata,
             schema=schema_name,
-            autoload=True,
             autoload_with=self.engine,
         )
 
     def load(self):
         """Load the table data from the database."""
-        query = select([self.table])
+        query = select(self.table)
         return pd.read_sql(query, self.connection, index_col=self.index_col)
 
     def write(self, row_id, result=None, exception=None, **input_values):
@@ -136,6 +135,7 @@ def write(self, row_id, result=None, exception=None, **input_values):
 
         query = insert(self.table).values(dict(**{self.index_col: row_id}, **vals, **input_values))
         self.connection.execute(query)
+        self.connection.connection.commit()
 
     def write_batch(self, columns, data):
         """Write entries from a list of lists into the table."""

commitlint.config.js

@@ -25,6 +25,7 @@ module.exports = {
 				'Fix',
 				'Perf',
 				'Refactor',
+				'Release',
 				'Revert',
 				'Style',
 				'Test',
@@ -95,6 +96,11 @@ module.exports = {
 						title: 'Reverts',
 						emoji: '🗑',
 					},
+					Release: {
+						description: 'Release commit',
+						title: 'Release',
+						emoji: '🎉',
+					},
 				},
 			},
 			scope: {

examples/large_computation.py

@@ -1,3 +1,4 @@
+"""Example of large computation using BluePyParallel."""
 import sys
 import time
 
@@ -9,7 +10,7 @@
 
 
 def func(row):
-    """Trivial computation"""
+    """Trivial computation."""
     time.sleep(1)
 
     if row["data"] in [1, 3]:

pyproject.toml

@@ -14,7 +14,6 @@ target-version = [
     "py38",
     "py39",
 ]
-include = 'bluepyparallel\/.*\.py$|tests\/.*\.py$|docs\/source\/conf\.py$|setup\.py$'
 
 # PYDOCSTYLE
 [tool.pydocstyle]
@@ -24,7 +23,6 @@ add-ignore = [
     "D107",
 ]
 convention = "google"
-match = "[bluepyparallel, tests, docs/source/conf.py, setup.py]"
 
 # ISORT
 [tool.isort]

setup.py

@@ -2,7 +2,7 @@
 import importlib.util
 from pathlib import Path
 
-from setuptools import find_packages
+from setuptools import find_namespace_packages
 from setuptools import setup
 
 spec = importlib.util.spec_from_file_location(
@@ -14,13 +14,15 @@
 VERSION = module.VERSION
 
 reqs = [
-    "pandas",
-    "ipyparallel<7",
-    "dask[dataframe, distributed]>=2.30",
-    "dask-mpi>=2.20",
-    "sqlalchemy>1.4",
-    "sqlalchemy-utils",
-    "tqdm",
+    "pandas>=1.3",
+    "ipyparallel>=6.3,<7",
+    "dask[dataframe, distributed]>=2021.11",
+    "dask-mpi>=2021.11",
+    "distributed>=2021.11",
+    "sqlalchemy>=1.4.24",
+    "sqlalchemy<2; python_version<'3.8'",
+    "sqlalchemy-utils>=0.37.2",
+    "tqdm>=3.7",
 ]
 
 doc_reqs = [
@@ -30,11 +32,11 @@
 ]
 
 test_reqs = [
-    "mpi4py",
-    "pytest",
-    "pytest-benchmark",
-    "pytest-cov",
-    "pytest-html",
+    "mpi4py>=3.0.1",
+    "pytest>=6.1",
+    "pytest-benchmark>=3.4",
+    "pytest-cov>=3",
+    "pytest-html>=3.1",
 ]
 
 setup(
@@ -50,14 +52,15 @@
         "Source": "https://bbpgitlab.epfl.ch/neuromath/bluepyparallel",
     },
     license="BBP-internal-confidential",
-    packages=find_packages(include=["bluepyparallel"]),
+    packages=find_namespace_packages(include=["bluepyparallel*"]),
     python_requires=">=3.7",
     version=VERSION,
     install_requires=reqs,
     extras_require={
         "docs": doc_reqs,
         "test": test_reqs,
     },
+    include_package_data=True,
     classifiers=[
         "Development Status :: 4 - Beta",
         "Intended Audience :: Developers",
@@ -66,6 +69,8 @@
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
-    include_package_data=True,
 )