bug fix (opening a config file in r+ mode) (#217)

* set release to true

* adds cgal and gmp to environment.yml

* fix write permission issue in config

* updates pybind11

.travis.yml

@@ -4,7 +4,7 @@ before_install:
   - sudo apt-get update
   - sudo apt-get install --yes build-essential
   - sudo apt-get install --yes git
-  - sudo apt-get install libcgal-dev libcgal-qt5-dev
+  - sudo apt-get install libmpfr-dev libgmp-dev libboost-all-dev
   - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
@@ -16,7 +16,7 @@ before_install:
   - source activate tyssue
   - conda install pytest pytest-cov
   - pip install coveralls nbval
-  
+
 install:
   - python setup.py install
 

INSTALL.md

@@ -35,47 +35,35 @@ With an Debian like system, this is achieved by:
 sudo apt install build-essential cmake g++
 ```
 
+### Download and install `tyssue` from source
+
+If you want to do that, I assume you allready know how to manage
+dependencies on your platform. The simplest way to manage dependencies is to use [`conda`](https://docs.conda.io/en/latest/miniconda.html) to manage the dependencies (you can use [`mamba`](https://github.com/mamba-org/mamba) as a faster alternative to conda).
 
-### Install CGAL
+Start by cloning tyssue recursively to also grab pybind11:
 
-You can use a pre-packaged version for your OS. For Debian:
 ```bash
-sudo apt install libcgal-dev
+git clone --recursive https://github.com/damcb/tyssue.git
+cd tyssue
 ```
-Note that you need version 4.7 or higher.
 
-If you need to install CGAL from source, here is a `cmake` command sufficient to later compile tyssue:
+Then create a virtual environement:
 
 ```bash
-cd CGAL # This is the directory where the CGAL archive was uncompressed
-mkdir build && cd build
-
-# needs qt5 for imageio
-cmake \
-  -DCMAKE_BUILD_TYPE=Release \
-  -DCMAKE_PREFIX_PATH=${PREFIX} \
-  -DCMAKE_INSTALL_PREFIX=${PREFIX} \
-  -DCGAL_INSTALL_LIB_DIR=lib \
-  -DWITH_CGAL_ImageIO=OFF -DWITH_CGAL_Qt5=OFF \
-  ..
-make install -j${CPU_COUNT}
+conda env create -f environment.yml
 ```
 
-
-### Download and install `tyssue` from source
-
-If you want to do that, I assume you allready know how to manage
-dependencies on your platform.
-
-```bash
-git clone --recursive https://github.com/damcb/tyssue.git
-cd tyssue/
+Then install python:
+```
 python setup.py install
 ```
 
+
+
 If all went well, you have successfully installed tyssue.
 
 ### Install testing utilities
+
 ```sh
 pip install pytest pytest-cov nbval
 ```

README.md

@@ -173,6 +173,8 @@ You can also install tyssue from PyPi, this is a CGAL-less version (pure python)
 
 `python -m pip install --user --upgrade tyssue`
 
+### From source
+
 See [INSTALL.md](INSTALL.md) for a step by step install, including the necessary python environment.
 
 

environment.yml

@@ -3,8 +3,11 @@ channels:
 - conda-forge
 
 dependencies:
+- pip
 - boost-cpp
 - mpfr
+- gmp
+- cgal
 - python>=3.6
 - numpy
 - scipy

tyssue/config/json_parser.py

@@ -11,7 +11,7 @@
 
 def load_spec(fname):
 
-    with open(fname, "r+") as config_file:
+    with open(fname, "r") as config_file:
         spec = json.load(config_file)
     return spec