Merge pull request #34 from delve-team/develop

Minor refactor, add docs, fix tests, etc.

.github/workflows/draft-pdf.yml

@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf

.github/workflows/tests.yaml

@@ -0,0 +1,53 @@
+name: Tests
+
+on:
+  push:
+    branches: [master]
+    tags: [v*]
+  pull_request:
+    branches: [master]
+
+jobs:
+  miniconda:
+    name: Miniconda ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        matrix:
+            os: ["ubuntu-latest", "windows-latest"]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test
+          channels: conda-forge,defaults
+          environment-file: environment.yml
+          python-version: 3.8
+          auto-activate-base: false
+      - shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+      - name: Lint
+        shell: bash -l {0}
+        run: |
+            conda install flake8
+            python -m flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+            python -m flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Run pytest
+        shell: bash -l {0}
+        run: |
+            pip install -r requirements/dev.txt
+            pip install -r requirements/docs.txt
+            pip install --upgrade pytest flake8 sphinx
+            pip install scipy --force-reinstall # for https://github.com/conda/conda/issues/6396
+            pip install .
+            conda install pytest
+            py.test . --cov-report=xml --cov=delve -vvv
+      - name: Codecov
+        uses: codecov/codecov-action@v2.0.2
+        with:
+          flags: unittests
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: false
+          verbose: false

.gitignore

@@ -90,6 +90,9 @@ ENV/
 env.bak/
 venv.bak/
 
+# Sphinx documentation
+docs/build/
+
 # Spyder project settings
 .spyderproject
 .spyproject
@@ -106,3 +109,5 @@ venv.bak/
 .DS_Store
 .idea/
 .vscode/
+
+*.pickle

.pre-commit-config.yaml

@@ -1,4 +1,27 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+    -   id: check-json
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+    -   id: check-added-large-files
+    -   id: requirements-txt-fixer
 -   repo: https://github.com/pre-commit/mirrors-yapf
     rev: stable  # Use the sha / tag you want to point at
     hooks:
     -   id: yapf
+-   repo: local
+    hooks:
+      - id: flake8
+        name: flake8
+        entry: python -m pflake8
+        language: system
+        types: [python]
+-   repo: git://github.com/timothycrosley/isort
+    rev: 5.8.0
+    hooks:
+    - id: isort
+      args: [ "--profile", "black" ]
+      exclude: ^scripts/old_notebooks

.readthedocs.yml

@@ -0,0 +1,13 @@
+version: 2
+sphinx:
+  configuration: docs/source/conf.py
+
+formats: all
+
+build:
+  image: latest
+
+python:
+  version: 3.7
+  install:
+    - requirements: requirements/docs.txt

delve/__init__.py

@@ -1,19 +1,16 @@
 try:
     import torch
-    from delve.torchcallback import CheckLayerSat
+
     from delve.tools import reconstruct_csv_from_npy_data
+    from delve.torchcallback import CheckLayerSat
 except ImportError:
     pass
 name = "delve"
 
-try:
-    from delve.writers import PrintWriter as console
-    from delve.writers import NPYWriter as npy
+try:    
     from delve.writers import CSVWriter as csv
-    from delve.writers import CSVandPlottingWriter as plot
-    from delve.writers import CSVandPlottingWriter as plotcsv
-
-    from delve.writers import CSVandPlottingWriter as csvplot
+    from delve.writers import NPYWriter as npy
+    from delve.writers import PrintWriter as console
     from delve.writers import TensorBoardWriter as tensorboard
 except ImportError:
     pass

delve/kerascallback.py

@@ -1,11 +1,9 @@
-import datetime
+import logging
 
 import keras
+import numpy as np
 import tensorflow as tf
-
 from keras import backend as K
-
-import numpy as np
 from numpy.linalg import LinAlgError
 
 
@@ -104,7 +102,6 @@ class CustomTensorBoard(tf.keras.callbacks.TensorBoard):
             specified for summary visualization.
         kwargs: Passed to tf.keras.callbacks.TensorBoard.
     """
-
     def __init__(self, user_defined_freq=0, **kwargs):
         self.user_defined_freq = user_defined_freq
         super(CustomTensorBoard, self).__init__(**kwargs)
@@ -126,7 +123,6 @@ def on_epoch_begin(self, epoch, logs=None):
 
         super(CustomTensorBoard, self).on_epoch_begin(epoch, logs=None)
 
-
     def on_epoch_end(self, epoch, logs=None):
         """Checks if summary ops should run next epoch, logs scalar summaries."""
 
@@ -150,7 +146,6 @@ class SaturationMetric(keras.callbacks.Callback):
             input_data: sample input to calculate layer saturation with, eg train
             print_freq
     """
-
     def __init__(self, model, input_data, print_freq=1):
         self.model = model
         self.input_data = input_data
@@ -174,11 +169,11 @@ def on_epoch_end(self, epoch, logs):
         if epoch > 2:
             for layer in layers:
                 try:
-                    print("epoch = %4d  layer = %r  sat = %0.2f%%" \
+                    logging.info("epoch = %4d  layer = %r  sat = %0.2f%%" \
                           % (epoch, layer, logs[layer]))
                     logs[layer] = self.preactivation_states[layer]
                 except Exception as e:
-                    print(e)
+                    logging.error(e)
 
 
 class SaturationLogger(keras.callbacks.Callback):
@@ -189,7 +184,6 @@ class SaturationLogger(keras.callbacks.Callback):
             input_data: sample input to calculate layer saturation with, eg train
             print_freq
     """
-
     def __init__(self, model, input_data, print_freq=1):
         self.model = model
         self.input_data = input_data
@@ -219,4 +213,4 @@ def on_epoch_end(self, epoch, logs):
             print_str = ""
             for layer in layers:
                 print_str += "{:^10}: %{:4.2f} |".format(layer, logs[layer])
-            print(print_str)
+            logging.info(print_str)

delve/metrics.py

@@ -64,4 +64,3 @@ def compute_diag_trace(cov: torch.Tensor) -> float:
     eig_vals, eigen_space = cov.symeig(True)
     eig_vals[eig_vals < 0] = 0
     return eig_vals.sum().unsqueeze(dim=0).cpu().numpy()[0]
-