Merge branch 'develop' into replace_fft and solve conflicts

Conflicts:
	src/aspire/basis/ffb_2d.py
	src/aspire/basis/fpswf_2d.py
	src/aspire/image/__init__.py
	src/aspire/noise/noise.py
	src/aspire/volume/__init__.py
	tests/test_fft.py

Author: junchaoxia

.travis.yml

@@ -1,21 +1,38 @@
-sudo: required
 language: python
-matrix:
+
+# manylinux2010 wheels are not found on xenial
+dist: bionic
+
+os:
+  - linux
+
+arch:
+  - amd64
+
+stages:
+  - check
+  - test
+  - deploy
+
+jobs:
   include:
     - python: 3.6
-      env:
-        - TOXENV=clean,py36-stable,coveralls,report
-        - TOXENV=py36-dev
+      env: TOXENV=clean,py36-stable,coveralls,report
+    - python: 3.6
+      env: TOXENV=py36-dev
     - python: 3.7
-      env:
-        - TOXENV=py37-stable
-        - TOXENV=py37-dev
+      env: TOXENV=py37-stable
+    - python: 3.7
+      env: TOXENV=py37-dev
+    - python: 3.8
+      env: TOXENV=py38-stable
     - python: 3.8
-      env:
-        - TOXENV=py38-stable
-        - TOXENV=py38-dev
-    - env: TOXENV=check
-    - env: TOXENV=docs
+      env: TOXENV=py38-dev
+    - python: 3.6
+      env: TOXENV=check
+    - python: 3.6
+      env: TOXENV=docs
+
 install:
   - pip install -U tox tox-travis
 

setup.py

@@ -24,7 +24,7 @@ def read(fname):
     author_email="[email protected]",
     install_requires=[
         "click",
-        "finufftpy",
+        "finufft",
         "importlib_resources>=1.0.2",
         "joblib",
         "jupyter",
@@ -54,7 +54,7 @@ def read(fname):
             "black",
             "bumpversion",
             "check-manifest",
-            "flake8",
+            "flake8>=3.7.0",
             "isort",
             "pyflakes",
             "pydocstyle",

src/aspire/__init__.py

@@ -6,8 +6,8 @@
 from importlib_resources import read_text
 
 import aspire
+from aspire.config import Config
 from aspire.exceptions import handle_exception
-from aspire.utils.config import Config
 
 # version in maj.min.bld format
 __version__ = "0.6.0"

src/aspire/abinitio/__init__.py

@@ -0,0 +1,2 @@
+from .commonline_base import CLOrient3D
+from .commonline_sync import CLSyncVoting

src/aspire/orientation/__init__.py renamed to src/aspire/abinitio/commonline_base.py

@@ -5,7 +5,7 @@
 import scipy.sparse as sparse
 
 from aspire import config
-from aspire.basis.polar_2d import PolarBasis2D
+from aspire.basis import PolarBasis2D
 from aspire.source import ArrayImageSource
 from aspire.utils.coor_trans import common_line_from_rots
 from aspire.utils.random import choice

src/aspire/orientation/commonline_ev.py renamed to src/aspire/abinitio/commonline_ev.py

@@ -1,6 +1,6 @@
 import logging
 
-from aspire.orientation import CLOrient3D
+from aspire.abinitio import CLOrient3D
 
 logger = logging.getLogger(__name__)
 

src/aspire/orientation/commonline_gcar.py renamed to src/aspire/abinitio/commonline_gcar.py

@@ -1,6 +1,6 @@
 import logging
 
-from aspire.orientation import CLOrient3D
+from aspire.abinitio import CLOrient3D
 
 logger = logging.getLogger(__name__)
 

src/aspire/orientation/commonline_lud.py renamed to src/aspire/abinitio/commonline_lud.py

@@ -1,6 +1,6 @@
 import logging
 
-from aspire.orientation import CLOrient3D
+from aspire.abinitio import CLOrient3D
 
 logger = logging.getLogger(__name__)
 

src/aspire/orientation/commonline_sdp.py renamed to src/aspire/abinitio/commonline_sdp.py

@@ -1,6 +1,6 @@
 import logging
 
-from aspire.orientation import CLOrient3D
+from aspire.abinitio import CLOrient3D
 
 logger = logging.getLogger(__name__)
 

src/aspire/orientation/commonline_sync.py renamed to src/aspire/abinitio/commonline_sync.py

@@ -3,7 +3,7 @@
 import numpy as np
 from scipy.spatial.transform import Rotation
 
-from aspire.orientation import CLOrient3D
+from aspire.abinitio import CLOrient3D
 from aspire.utils import ensure
 from aspire.utils.matlab_compat import stable_eigsh