Merge pull request #13 from plstcharles/fix-sliding-window-dataset

fix sliding window dataset

CHANGELOG.rst

@@ -6,10 +6,16 @@ Changelog
 `Unreleased <http://github.com/plstcharles/thelper/tree/master>`_ (latest)
 ----------------------------------------------------------------------------------
 
+`0.5.0-rc1 <http://github.com/plstcharles/thelper/tree/v0.5.0-rc1>`_ (2020/07/07)
+----------------------------------------------------------------------------------
+
 * Fix version comparison check when validating configuration and/or checkpoint against package version.
   Version can now have a release part which was not considered.
+* Fix incorrect calculation of sample coordinates in ``thelper.data.geo.parsers.SlidingWindowDataset``.
+* Remove ``not_skip = __init__.py`` config option for ``isort`` since ``__init__.py`` is included since ``4.3.5``.
+  Also force ``isort<5`` since many import checks break suddenly (e.g.: direct import with `as` alias break).
 
-`0.5.0-rc <http://github.com/plstcharles/thelper/tree/0.5.0-rc>`_ (%Y/%m/%d)
+`0.5.0-rc0 <http://github.com/plstcharles/thelper/tree/v0.5.0-rc0>`_ (2020/04/25)
 ----------------------------------------------------------------------------------
 
 * Update this changelog to use rst links (renders on github and readthedocs)
@@ -18,17 +24,17 @@ Changelog
 * Add geo-related build instructions to travis-ci build steps
 * Add auto-documentation of makefile targets and docker related targets
 
-`0.4.7 <http://github.com/plstcharles/thelper/tree/0.4.7>`_ (2019/11/20)
+`0.4.7 <http://github.com/plstcharles/thelper/tree/v0.4.7>`_ (2019/11/20)
 ----------------------------------------------------------------------------------
 
 * Removed optional dependencies from conda build env
 
-`0.4.6 <http://github.com/plstcharles/thelper/tree/0.4.6>`_ (2019/11/20)
+`0.4.6 <http://github.com/plstcharles/thelper/tree/v0.4.6>`_ (2019/11/20)
 ----------------------------------------------------------------------------------
 
 * Travis deploy test w/ split conda/docker stages
 
-`0.4.5 <http://github.com/plstcharles/thelper/tree/0.4.5>`_ (2019/11/18)
+`0.4.5 <http://github.com/plstcharles/thelper/tree/v0.4.5>`_ (2019/11/18)
 ----------------------------------------------------------------------------------
 
 * Split travis deploy stage into two phases
@@ -37,7 +43,7 @@ Changelog
 * Update all matplotlib plots to use 160 dpi by default
 * Refactor trainer data/metric writer to save all viz data
 
-`0.4.4 <http://github.com/plstcharles/thelper/tree/0.4.4>`_ (2019/11/18)
+`0.4.4 <http://github.com/plstcharles/thelper/tree/v0.4.4>`_ (2019/11/18)
 ----------------------------------------------------------------------------------
 
 * Added viz pkg w/ t-SNE & UMAP support for in-trainer usage
@@ -54,12 +60,12 @@ Changelog
 * Added efficientnet 3rd-party module wrapper
 * Fixed potential conflicts in task class names ordering
 
-`0.4.3 <http://github.com/plstcharles/thelper/tree/0.4.3>`_ (2019/11/06)
+`0.4.3 <http://github.com/plstcharles/thelper/tree/v0.4.3>`_ (2019/11/06)
 ----------------------------------------------------------------------------------
 
 * Fixed pytest-mock scope usage in metrics utests
 
-`0.4.2 <http://github.com/plstcharles/thelper/tree/0.4.2>`_ (2019/11/06)
+`0.4.2 <http://github.com/plstcharles/thelper/tree/v0.4.2>`_ (2019/11/06)
 ----------------------------------------------------------------------------------
 
 * Updated common resnet impl to support segmentation heads
@@ -71,12 +77,12 @@ Changelog
 * Update segmentation trainer to use long-typed label maps
 * Cleaned up augmentor/albumentations demo configurations
 
-`0.4.1 <http://github.com/plstcharles/thelper/tree/0.4.1>`_ (2019/10/15)
+`0.4.1 <http://github.com/plstcharles/thelper/tree/v0.4.1>`_ (2019/10/15)
 ----------------------------------------------------------------------------------
 
 * Removed travis check in deploy stage for master branch
 
-`0.4.0 <http://github.com/plstcharles/thelper/tree/0.4.0>`_ (2019/10/11)
+`0.4.0 <http://github.com/plstcharles/thelper/tree/v0.4.0>`_ (2019/10/11)
 ----------------------------------------------------------------------------------
 
 * Added geo subpackage
@@ -88,14 +94,14 @@ Changelog
 * Merged 3rdparty configs into setup.cfg
 * Updated travis to rely on makefile directly
 
-`0.3.14 <http://github.com/plstcharles/thelper/tree/0.3.14>`_ (2019/09/30)
+`0.3.14 <http://github.com/plstcharles/thelper/tree/v0.3.14>`_ (2019/09/30)
 ----------------------------------------------------------------------------------
 
 * Added extra logging calls in trainer and framework utils
 * Cleaned up data configuration parsing logger calls
 * Bypassed full device check when specific one is requested
 
-`0.3.13 <http://github.com/plstcharles/thelper/tree/0.3.13>`_ (2019/09/26)
+`0.3.13 <http://github.com/plstcharles/thelper/tree/v0.3.13>`_ (2019/09/26)
 ----------------------------------------------------------------------------------
 
 * Moved drawing utilities to new module
@@ -105,18 +111,18 @@ Changelog
 * Added support for root directory specification via config
 * Updated config load/save to make naming optional
 
-`0.3.12 <http://github.com/plstcharles/thelper/tree/0.3.12>`_ (2019/09/13)
+`0.3.12 <http://github.com/plstcharles/thelper/tree/v0.3.12>`_ (2019/09/13)
 ----------------------------------------------------------------------------------
 
 * Fixed potential issue when reinstantiating custom ResNet
 * Fixed ClassifLogger prediction logger w/o groundtruth
 
-`0.3.11 <http://github.com/plstcharles/thelper/tree/0.3.11>`_ (2019/09/09)
+`0.3.11 <http://github.com/plstcharles/thelper/tree/v0.3.11>`_ (2019/09/09)
 ----------------------------------------------------------------------------------
 
 * Add cli/config override for task compatibility mode setting
 
-`0.3.10 <http://github.com/plstcharles/thelper/tree/0.3.10>`_ (2019/09/05)
+`0.3.10 <http://github.com/plstcharles/thelper/tree/v0.3.10>`_ (2019/09/05)
 ----------------------------------------------------------------------------------
 
 * Cleaned up dependency lists, docstrings
@@ -127,7 +133,7 @@ Changelog
 * Fixed exponential parsing with pyyaml
 * Fixed bbox display when using integer coords values
 
-`0.3.9 <http://github.com/plstcharles/thelper/tree/0.3.9>`_ (2019/08/20)
+`0.3.9 <http://github.com/plstcharles/thelper/tree/v0.3.9>`_ (2019/08/20)
 ----------------------------------------------------------------------------------
 
 * Fixed collate issues for pytorch >= 1.2
@@ -139,15 +145,15 @@ Changelog
 * Cleaned up shared interfaces to fix circular dependencies
 * Added detection (bbox) logger class
 
-`0.3.8 <http://github.com/plstcharles/thelper/tree/0.3.8>`_ (2019/08/08)
+`0.3.8 <http://github.com/plstcharles/thelper/tree/v0.3.8>`_ (2019/08/08)
 ----------------------------------------------------------------------------------
 
 * Fixed nn modules constructor args forwarding
 * Updated class importer to allow parsing of non-package dirs
 * Fixed file-based logging from submodules (e.g. for all data)
 * Cleaned and API-fied the CLI entrypoints for external use
 
-`0.3.7 <http://github.com/plstcharles/thelper/tree/0.3.7>`_ (2019/07/31)
+`0.3.7 <http://github.com/plstcharles/thelper/tree/v0.3.7>`_ (2019/07/31)
 ----------------------------------------------------------------------------------
 
 * Fixed travis timeouts on long deploy operations
@@ -157,7 +163,7 @@ Changelog
 * Cleaned up matplotlib use and show/block across draw functions
 * Fixed various dependency and logging issues
 
-`0.3.6 <http://github.com/plstcharles/thelper/tree/0.3.6>`_ (2019/07/26)
+`0.3.6 <http://github.com/plstcharles/thelper/tree/v0.3.6>`_ (2019/07/26)
 ----------------------------------------------------------------------------------
 
 * Fixed torch version checks in custom default collate impl
@@ -166,7 +172,7 @@ Changelog
 * Added pretrained opt to default resnet impl
 * Fixed objdetect trainer display and prediction callbacks
 
-`0.3.5 <http://github.com/plstcharles/thelper/tree/0.3.5>`_ (2019/07/23)
+`0.3.5 <http://github.com/plstcharles/thelper/tree/v0.3.5>`_ (2019/07/23)
 ----------------------------------------------------------------------------------
 
 * Refactored metrics/consumers into separate interfaces
@@ -176,33 +182,33 @@ Changelog
 * Cleaned drawing functions args wrt callback refactoring
 * Added eval module to optim w/ pascalvoc evaluation funcs
 
-`0.3.4 <http://github.com/plstcharles/thelper/tree/0.3.4>`_ (2019/07/12)
+`0.3.4 <http://github.com/plstcharles/thelper/tree/v0.3.4>`_ (2019/07/12)
 ----------------------------------------------------------------------------------
 
 * Fixed issues when reloading objdet model checkpoints
 * Fixed issues when trying to use missing color maps
 * Fixed backward compat issues when reloading old tasks
 * Cleaned up object detection drawing utilities
 
-`0.3.3 <http://github.com/plstcharles/thelper/tree/0.3.3>`_ (2019/07/09)
+`0.3.3 <http://github.com/plstcharles/thelper/tree/v0.3.3>`_ (2019/07/09)
 ----------------------------------------------------------------------------------
 
 * Fixed travis conda build dependencies & channels
 
-`0.3.2 <http://github.com/plstcharles/thelper/tree/0.3.2>`_ (2019/07/05)
+`0.3.2 <http://github.com/plstcharles/thelper/tree/v0.3.2>`_ (2019/07/05)
 ----------------------------------------------------------------------------------
 
 * Update documentation use cases (model export) & faq
 * Cleanup module base class config backup
 * Fixed docker build and automated it via travis
 
-`0.3.1 <http://github.com/plstcharles/thelper/tree/0.3.1>`_ (2019/06/17)
+`0.3.1 <http://github.com/plstcharles/thelper/tree/v0.3.1>`_ (2019/06/17)
 ----------------------------------------------------------------------------------
 
 * Fix metrics RawPredictions not returning predictions during eval
 * Fix parsing of checkpoint base path
 
-`0.3.0 <http://github.com/plstcharles/thelper/tree/0.3.0>`_ (2019/06/12)
+`0.3.0 <http://github.com/plstcharles/thelper/tree/v0.3.0>`_ (2019/06/12)
 ----------------------------------------------------------------------------------
 
 * Added dockerfile for containerized builds
@@ -213,7 +219,7 @@ Changelog
 * Added lots of new unit tests & docstrings
 * Cleaned up transform & display operations
 
-`0.2.8 <http://github.com/plstcharles/thelper/tree/0.2.8>`_ (2019/03/17)
+`0.2.8 <http://github.com/plstcharles/thelper/tree/v0.2.8>`_ (2019/03/17)
 ----------------------------------------------------------------------------------
 
 * Cleaned up build tools & docstrings throughout api
@@ -223,34 +229,34 @@ Changelog
 * Added fully convolutional resnet implementation
 * Fixup various issues related to fine-tuning via 'resume'
 
-`0.2.7 <http://github.com/plstcharles/thelper/tree/0.2.7>`_ (2019/02/04)
+`0.2.7 <http://github.com/plstcharles/thelper/tree/v0.2.7>`_ (2019/02/04)
 ----------------------------------------------------------------------------------
 
 * Updated conda build recipe for python variants w/ auto upload
 
-`0.2.6 <http://github.com/plstcharles/thelper/tree/0.2.6>`_ (2019/01/31)
+`0.2.6 <http://github.com/plstcharles/thelper/tree/v0.2.6>`_ (2019/01/31)
 ----------------------------------------------------------------------------------
 
 * Added framework checkpoint/configuration migration utilities
 * Fixed minor config parsing backward compatibility issues
 * Fixed minor bugs related to query & drawing utilities
 
-`0.2.5 <http://github.com/plstcharles/thelper/tree/0.2.5>`_ (2019/01/29)
+`0.2.5 <http://github.com/plstcharles/thelper/tree/v0.2.5>`_ (2019/01/29)
 ----------------------------------------------------------------------------------
 
 * Fix travis-ci conda build/env path
 
-`0.2.4 <http://github.com/plstcharles/thelper/tree/0.2.4>`_ (2019/01/29)
+`0.2.4 <http://github.com/plstcharles/thelper/tree/v0.2.4>`_ (2019/01/29)
 ----------------------------------------------------------------------------------
 
 * Fix travis-ci conda channel setup
 
-`0.2.3 <http://github.com/plstcharles/thelper/tree/0.2.3>`_ (2019/01/29)
+`0.2.3 <http://github.com/plstcharles/thelper/tree/v0.2.3>`_ (2019/01/29)
 ----------------------------------------------------------------------------------
 
 * Fix ``openssl`` dependency
 
-`0.2.2 <http://github.com/plstcharles/thelper/tree/0.2.2>`_ (2019/01/29)
+`0.2.2 <http://github.com/plstcharles/thelper/tree/v0.2.2>`_ (2019/01/29)
 ----------------------------------------------------------------------------------
 
 * Fixed travis-ci matrix configuration
@@ -261,7 +267,7 @@ Changelog
 * Fixed openssl dependency issues for travis tox check jobs
 * Updated travis post-deploy to try to fix conda packaging (wip)
 
-`0.2.1 <http://github.com/plstcharles/thelper/tree/0.2.1>`_ (2019/01/24)
+`0.2.1 <http://github.com/plstcharles/thelper/tree/v0.2.1>`_ (2019/01/24)
 ----------------------------------------------------------------------------------
 
 * Added typedef module & cleaned up parameter inspections
@@ -270,7 +276,7 @@ Changelog
 * Updated all trainers/schedulers to rely on 0-based indexing
 * Updated travis/rtd configs for auto-deploy & 3.6 support
 
-`0.2.0 <http://github.com/plstcharles/thelper/tree/0.2.0>`_ (2019/01/15)
+`0.2.0 <http://github.com/plstcharles/thelper/tree/v0.2.0>`_ (2019/01/15)
 ----------------------------------------------------------------------------------
 
 * Added regression/segmentation tasks and trainers
@@ -285,13 +291,13 @@ Changelog
 * Added trainer support for loss computation via external members
 * Added utils to download/verify/extract files
 
-`0.1.1 <http://github.com/plstcharles/thelper/tree/0.1.1>`_ (2019/01/14)
+`0.1.1 <http://github.com/plstcharles/thelper/tree/v0.1.1>`_ (2019/01/14)
 ----------------------------------------------------------------------------------
 
 * Minor fixups and updates for CCFB02 compatibility
 * Added RawPredictions metric to fetch data from trainers
 
-`0.1.0 <http://github.com/plstcharles/thelper/tree/0.1.0>`_ (2018/11/28)
+`0.1.0 <http://github.com/plstcharles/thelper/tree/v0.1.0>`_ (2018/11/28)
 ----------------------------------------------------------------------------------
 
 * Fixed readthedocs sphinx auto-build w/ mocking.
@@ -305,14 +311,14 @@ Changelog
 * Refactored task interfaces to allow merging.
 * Simplified model fine-tuning via checkpoints.
 
-`0.0.2 <http://github.com/plstcharles/thelper/tree/0.0.2>`_ (2018/10/18)
+`0.0.2 <http://github.com/plstcharles/thelper/tree/v0.0.2>`_ (2018/10/18)
 ----------------------------------------------------------------------------------
 
 * Completed first documentation pass.
 * Fixed travis/rtfd builds.
 * Fixed device mapping/loading issues.
 
-`0.0.1 <http://github.com/plstcharles/thelper/tree/0.0.1>`_ (2018/10/03)
+`0.0.1 <http://github.com/plstcharles/thelper/tree/v0.0.1>`_ (2018/10/03)
 ----------------------------------------------------------------------------------
 
 * Initial release (work in progress).

Dockerfile

@@ -2,7 +2,7 @@ FROM nvidia/cuda:10.0-cudnn7-devel-ubuntu16.04
 LABEL name="thelper"
 LABEL description="Training framework and CLI for PyTorch-based machine learning projects"
 LABEL vendor="Centre de Recherche Informatique de Montréal / Computer Research Institute of Montreal (CRIM)"
-LABEL version="0.5.0-rc"
+LABEL version="0.5.0-rc1"
 
 ARG PYTHON_VERSION=3.7
 

README.rst

@@ -24,9 +24,9 @@ Overview
     :alt: Travis-CI Build Status
     :target: https://travis-ci.org/plstcharles/thelper
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/plstcharles/thelper/v0.5.0-rc.svg
+.. |commits-since| image:: https://img.shields.io/github/commits-since/plstcharles/thelper/v0.5.0-rc1.svg
     :alt: Commits since latest release
-    :target: https://github.com/plstcharles/thelper/compare/v0.5.0-rc...master
+    :target: https://github.com/plstcharles/thelper/compare/v0.5.0-rc1...master
 
 .. |readthedocs| image:: https://readthedocs.org/projects/thelper/badge/?version=latest
     :alt: Documentation Build Status

ci/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "thelper" %}
-{% set version = "0.5.0-rc" %}
+{% set version = "0.5.0-rc1" %}
 
 package:
   name: "{{ name|lower }}"

docs/src/conf.py

@@ -23,7 +23,7 @@
 project = 'thelper'
 copyright = '2018, Pierre-Luc St-Charles'
 author = 'Pierre-Luc St-Charles'
-version = release = '0.5.0-rc'
+version = release = '0.5.0-rc1'
 
 
 # -- General configuration ---------------------------------------------------

requirements-dev.txt

@@ -4,7 +4,7 @@ check-manifest
 flake8
 readme-renderer
 pygments
-isort
+isort>=4.3.5,<5
 mock
 pyopenssl
 pytest