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Standardise how paths are handled  (#189)

* ads_utils: update module to pathlib

and do some reformatting.

On branch maf88/154-standardize-paths-management
Changes to be committed:
	modified:   AxonDeepSeg/ads_utils.py
	modified:   test/test_ads_utils.py

* Revert styling changes

* Revert more styling changes

* ads_utils: Refactor to use tempfile and pathlib

* test_dataset_building.py:  Refactor to use pathlib

* Refactor to pathlib and remove unused imports

* test_launch_morph[...]:  Refactor to use pathlib

* test_launch_perf[...]: Refactor to use pathlib

* test_noise_simulation: Refactor to use pathlib

* test_segmentation_scoring: Refactor to use pathlib

* statistics_generation and test_st[...] use pathlib

* test_generate_axons_from_myelin: refact to pathlib

* test_get_masks: use pathib

* test_merge_masks: use pathlib

* test_visualize.py : use pathlib

* test_ads_utils.py: use pathlib

* Fix typo

* test_config_tools.py: use pathlib

* FIX convert Path to str for specific functions

* Fix  missing () in test_config_tools.py

* test_segment.py: Update to pathlib

* test_train_network.py: Refactor to use pathlib

* setup.py: Refactor path handling to pathlib

* config_tools.py: use pathlib

* integrity_test.py: use pathlib

* input_data.py: use pathlib

* integrity_test: FIX wrong syntax for path

* input_data.py: FIX dataset size eval and docstring

* conf.py: use pathlib

* merge_masks.py: use pathlib

* get_masks.py: Refactor to handle paths correctly

* submission_generator_tools.py:  refactor 2 pathlib

* train_network.py: Refactor to pathlib

* test_train_network: FIX Path to str conversion

* train_network: FIX  tf.train.Saver.save() param type

* segment.py : update to pathlib

* apply_model.py: use pathlib

* apply_model.py: FIX bad indent

* dataset_building.py: Refactor to pathlib

* mapping_results.py: use pathlib

* get_masks.py: use pathl... (continued)

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