Merge branch 'master' of https://github.com/tbepler/topaz

tbepler · Mar 21, 2019 · 70f5f04 · 70f5f04
2 parents 82ddc6f + b26e4ab
commit 70f5f04
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diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,2 @@
+include README.md
+include topaz/gui/topaz.html
diff --git a/README.md b/README.md
@@ -3,9 +3,7 @@ A pipeline for particle detection in cryo-electron microscopy images using convo
 
 # Prerequisites
 
-- Linux for installation from source, or any modern operating system for Docker installation.
-
-- An Nvidia GPU.
+- An Nvidia GPU with CUDA support for GPU acceleration.
 
 - Basic Unix/Linux knowledge.
 
@@ -104,7 +102,7 @@ Tested with python 3.6 and 2.7
 - scipy (>= 0.19.1)
 - scikit-learn (>= 0.19.0)
 
-Easy installation of dependencies
+Easy installation of dependencies with conda
 ```
 conda install numpy pandas scikit-learn
 conda install -c soumith pytorch=0.2.0 torchvision
@@ -127,6 +125,11 @@ Move to the source code directory
 cd topaz
 ```
 
+By default, this will be the most recent version of the topaz source code. To install a specific older version, checkout that commit. For example, for v0.1.0 of Topaz:
+```
+git checkout v0.1.0
+```
+
 Install Topaz into your Python path including the topaz command line interface
 ```
 pip install .
@@ -406,7 +409,7 @@ optional arguments:
 
 </p></details>
 
-# References
+# Reference
 
 Bepler, T., Morin, A., Brasch, J., Shapiro, L., Noble, A.J., Berger, B. (2018). Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. arXiv. https://arxiv.org/abs/1803.08207
 

diff --git a/conda-build/meta-v0.0.0.yaml b/conda-build/meta-v0.0.0.yaml
@@ -0,0 +1,33 @@
+package:
+    name: "topaz"
+    version: {{ GIT_DESCRIBE_TAG }}
+
+source:
+    git_url: https://github.com/tbepler/topaz.git
+    git_tag: v0.0.0
+
+requirements:
+    build:
+        - python
+        - setuptools
+    run:
+        - python
+        - argparse #[py26]
+        - numpy>=0.11
+        - pandas
+        - scikit-learn>=0.19.0
+        - pillow
+        - pytorch=0.2.0
+        - torchvision
+
+
+build:
+    noarch: python
+    number: 2
+    script: "{{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt"
+
+
+about:
+    home: https://github.com/tbepler/topaz
+    license: GPLv3
+    license_file: LICENSE
diff --git a/meta.yaml → conda-build/meta.yaml b/meta.yaml → conda-build/meta.yaml
@@ -1,10 +1,12 @@
+{% set data = load_setup_py_data() %}
+
 package:
     name: "topaz"
-    version: "0.0.0"
+    version: {{ data.get('version') }}
 
 source:
     git_url: https://github.com/tbepler/topaz.git
-    git_tag: v0.0.0
+    git_tag: master
 
 requirements:
     build:
@@ -23,7 +25,7 @@ requirements:
 
 build:
     noarch: python
-    number: 3
+    number: 0
     script: "{{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt"
 
 

diff --git a/setup.py b/setup.py
@@ -1,7 +1,7 @@
 from setuptools import setup, find_packages
 
 name = 'topaz'
-version = '0.0.0'
+version = '0.1.0'
 
 description = 'Particle picking with positive-unlabeled CNNs'
 long_description = 'Particle picking software for single particle cryo-electron microscopy using convoluational neural networks and positive-unlabeled learning.'

diff --git a/topaz/_version.py b/topaz/_version.py
@@ -1 +1 @@
-__version__ = "0.1.0a"
+__version__ = "0.1.0"
diff --git a/topaz/commands/gui.py b/topaz/commands/gui.py
@@ -2,7 +2,6 @@
 
 import os
 import sys
-import topaz.main
 
 name = 'gui'
 help = 'opens the topaz GUI in a web browser'
@@ -17,8 +16,8 @@ def main(args):
     import webbrowser
 
     # where is the GUI
-    root = os.path.dirname(topaz.main.__file__)
-    root = os.path.dirname(root)
+    root = os.path.dirname(__file__) # this is the commands dir
+    root = os.path.dirname(root) # now in the topaz root dir
     gui_path = os.path.join(root, 'gui', 'topaz.html')
 
     # open the GUI