Merge pull request #29 from brainglobe/fixing_tests

Moved atlas_gen to separate package

.travis.yml

@@ -12,64 +12,43 @@ stages:
 jobs:
   include:
     - stage: test
-      name: "Ubuntu Bionic python 3.6"
+      name: "Ubuntu Xenial python 3.6"
       language: python
       os: linux
       env: MINICONDA_URL=http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-      dist: bionic
+      dist: xenial
       python: 3.6
       before_install: source travis/install_unix.sh
       script: bash travis/test.sh
+
     - stage: test
-      name: "Ubuntu Bionic python 3.7"
-      language: python
-      os: linux
-      env: MINICONDA_URL=http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-      dist: bionic
-      python: 3.7
-      before_install: source travis/install_unix.sh
-      script: bash travis/test.sh
-    - stage: test
-      name: "Ubuntu Xenial python 3.6"
+      name: "Ubuntu Xenial python 3.7"
       language: python
       os: linux
       env: MINICONDA_URL=http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
       dist: xenial
-      python: 3.6
+      python: 3.7
       before_install: source travis/install_unix.sh
       script: bash travis/test.sh
+
     - stage: test
-      name: "Ubuntu Xenial python 3.7"
+      name: "Ubuntu Xenial python 3.8"
       language: python
       os: linux
       env: MINICONDA_URL=http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
       dist: xenial
-      python: 3.7
+      python: 3.8
       before_install: source travis/install_unix.sh
       script: bash travis/test.sh
-    - stage: test
-      name: "Windows Python 3.6"
-      language: shell
-      env: TRAVIS_PYTHON_VERSION=3.6
-      os: windows
-      before_install: source travis/install_windows.sh
-      script: bash travis/test.sh
+
     - stage: test
       name: "Windows Python 3.7"
       language: shell
       env: TRAVIS_PYTHON_VERSION=3.7
       os: windows
       before_install: source travis/install_windows.sh
       script: bash travis/test.sh
-    - stage: test
-      name: "macOS Python 3.6"
-      os: osx
-      language: shell
-      env:
-      - TRAVIS_PYTHON_VERSION=3.6
-      - MINICONDA_URL=https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
-      before_install: source travis/install_unix.sh
-      script: bash travis/test.sh
+
     - stage: test
       name: "macOS Python 3.7"
       os: osx
@@ -79,6 +58,18 @@ jobs:
       - MINICONDA_URL=https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
       before_install: source travis/install_unix.sh
       script: bash travis/test.sh
+
+    - stage: test
+      name: "Lint"
+      language: python
+      os: linux
+      env: MINICONDA_URL=http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+      dist: xenial
+      python: 3.7
+      before_install: source travis/install_unix.sh
+      script: bash travis/lint.sh
+
+
     - stage: deploy
       os: bionic
       name: "Deploy Linux"

MANIFEST.in

@@ -0,0 +1,3 @@
+include LICENSE
+include README.md
+include requirements.txt

atlas_gen/__init__.py

@@ -0,0 +1 @@
+from atlas_gen import mesh_utils

brainatlas_api/atlas_gen/atlas_scripts/test_atlas.py → atlas_gen/atlas_scripts/example_atlas.py

@@ -7,12 +7,9 @@
 import json
 import shutil
 
-from brainatlas_api.atlas_gen import (
-    save_anatomy,
-    save_annotation,
-    descriptors,
-    wrapup_atlas_from_dir,
-)
+from atlas_gen.stacks import save_anatomy, save_annotation
+from atlas_gen.wrapup import wrapup_atlas_from_dir
+from brainatlas_api import descriptors
 
 # Specify information about the atlas:
 RES_UM = 100

brainatlas_api/atlas_gen/atlas_scripts/fishatlas_atlas.py → atlas_gen/atlas_scripts/fishatlas_atlas.py

@@ -1,4 +1,7 @@
-from fishatlas_utils import add_path_inplace, collect_all_inplace
+from atlas_gen.atlas_scripts.fishatlas_utils import (
+    add_path_inplace,
+    collect_all_inplace,
+)
 
 from pathlib import Path
 import tempfile

brainatlas_api/atlas_gen/atlas_scripts/humanatlas.py → atlas_gen/atlas_scripts/humanatlas.py

@@ -12,12 +12,12 @@
 from brainatlas_api.atlas_gen import (
     save_anatomy,
     save_annotation,
-    descriptors,
     wrapup_atlas_from_dir,
     volume_utils,
-    mesh_utils,
     get_structure_children,
 )
+from atlas_gen import mesh_utils
+from brainatlas_api import descriptors
 from brainatlas_api.structures.structure_tree import StructureTree
 
 

brainatlas_api/atlas_gen/atlas_scripts/kim_unified_atlas.py → atlas_gen/atlas_scripts/kim_unified_atlas.py

@@ -16,11 +16,11 @@
 from brainio.brainio import load_any
 from allensdk.core.reference_space_cache import ReferenceSpaceCache
 
-from brainatlas_api.atlas_gen.volume_utils import (
+from atlas_gen.volume_utils import (
     extract_volume_surface,
     load_labelled_volume,
 )
-from brainatlas_api.atlas_gen.metadata_utils import create_metadata_files
+from atlas_gen.metadata_utils import create_metadata_files
 
 
 paxinos_allen_directory = Path(

brainatlas_api/atlas_gen/atlas_scripts/ratatlas.py → atlas_gen/atlas_scripts/ratatlas.py

@@ -1,8 +1,8 @@
-from brainatlas_api.atlas_gen.volume_utils import (
+from atlas_gen.volume_utils import (
     extract_volume_surface,
     load_labelled_volume,
 )
-from brainatlas_api.atlas_gen.metadata_utils import create_metadata_files
+from atlas_gen.metadata_utils import create_metadata_files
 from brainio.brainio import load_any
 
 

brainatlas_api/atlas_gen/stacks.py → atlas_gen/stacks.py

@@ -1,5 +1,5 @@
 import tifffile
-from brainatlas_api.atlas_gen import descriptors
+from brainatlas_api import descriptors
 
 
 def write_stack(stack, filename):

brainatlas_api/atlas_gen/structures.py → atlas_gen/structures.py

@@ -1,6 +1,4 @@
-from brainatlas_api.atlas_gen.descriptors import (
-    STRUCTURE_TEMPLATE as STEMPLATE,
-)
+from brainatlas_api.descriptors import STRUCTURE_TEMPLATE as STEMPLATE
 from brainatlas_api.structures.structure_tree import StructureTree
 
 

brainatlas_api/atlas_gen/wrapup.py → atlas_gen/wrapup.py

@@ -3,7 +3,7 @@
 from brainatlas_api.utils import read_tiff, read_json
 from .metadata import generate_metadata_dict
 from .structures import check_struct_consistency
-from . import descriptors
+from brainatlas_api import descriptors
 import tarfile
 import shutil
 

brainatlas_api/core.py

@@ -4,7 +4,7 @@
 from brainatlas_api.utils import read_json, read_tiff, make_hemispheres_stack
 from brainatlas_api.structures.structure_tree import StructureTree
 from brainatlas_api.obj_utils import read_obj
-from brainatlas_api.atlas_gen.descriptors import (
+from brainatlas_api.descriptors import (
     METADATA_FILENAME,
     STRUCTURES_FILENAME,
     REFERENCE_FILENAME,

requirements.txt

@@ -0,0 +1,6 @@
+tqdm
+numpy
+tifffile
+treelib
+pandas
+requests

setup.py

@@ -1,7 +1,7 @@
 from setuptools import setup, find_namespace_packages
 
-requirements = ["tqdm", "numpy", "tifffile", "treelib", "pandas"]
-
+with open("requirements.txt") as f:
+    requirements = f.read().splitlines()
 
 setup(
     name="brainatlas-api",
@@ -41,6 +41,7 @@
         "Programming Language :: Python",
         "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
         "Intended Audience :: Developers",
         "Intended Audience :: Science/Research",
     ],

travis/lint.sh

@@ -0,0 +1,6 @@
+
+pip install black
+pip install flake8
+
+flake8
+black ./ -l 79 --target-version py37 --check

travis/test.sh

@@ -1,4 +1,7 @@
-pip install -e .[dev]
+pip install -r requirements.txt --no-cache-dir
+
+pip install pytest
+pip install pytest-cov
+
 conda info -a
-black ./ -l 79 --target-version py37 --check
-pytest --cov=brainatlas_api
+pytest --cov=brainatlas_api