Merge pull request #48 from jajcayn/feature/switch_gpflow_pypi

Feature/switch gpflow pypi
jajcayn · Mar 31, 2020 · 143080f · 143080f
2 parents ba7ae42 + 6256127
commit 143080f
Show file tree

Hide file tree

Showing 8 changed files with 466 additions and 481 deletions.
diff --git a/README.md b/README.md
@@ -24,13 +24,11 @@ Example of ternary partition tree after optimisation.
 `GPSO` package is tested and should run without any problems on python versions 3.6 and 3.7.
 
 ### One-liner
-Installation from PyPI is not possible, as `GPFlow` 2.0 is not on PyPI yet.
-
 For those who want to optimise right away just
 ```bash
-pip install git+https://github.com/jajcayn/pygpso
+pip install pygpso
 ```
-and go ahead! Make sure to check example notebooks in [the **examples** directory](examples/) to see how it works and what it can do. Or, alternatively, you can run interactive notebooks in binder: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jajcayn/pygpso.git/master?filepath=examples).
+and go ahead! Make sure to check example notebooks in [the **examples** directory](examples/) to see how it works and what it can do. Or, alternatively, you can run interactive notebooks in binder: [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/jajcayn/pygpso.git/master?filepath=examples
 
 ### Go proper
 When you are the type of girl or guy who likes to install packages properly, start by cloning (or forking) this repository, then installing all the dependencies and finally install the package itself
@@ -52,8 +50,7 @@ A guide on how to optimise and what can be done using this package is given as j
 
 The basic idea is to initialise the parameter space in which the optimisation is to be run and then iteratively dig deeper and evaluate the objective function when necessary
 ```python
-from gpso.param_space import ParameterSpace
-from gpso.optimisation import GPSOptimiser
+from gpso import ParameterSpace, GPSOptimiser
 
 
 def objective_function(params):
@@ -82,9 +79,7 @@ Plotting of the ternary tree (`gpso.plotting.plot_ternary_tree()`) requires `igr
 Support of saver (for saving models run, e.g. timeseries along with the optimisation) is provided by `PyTables` (and `pandas` if you're saving results to `DataFrame`s).
 
 ## Known bugs and future improvements
-* currently cannot be installed through `pip` from PyPI, since `GPFlow` 2.0 is not on PyPI yet
 * saving of GP surrogate is now hacky, as `GPFlow` not yet officially supports saving / loading of the models due to [bug in `tensorflow`](https://github.com/tensorflow/tensorflow/issues/34908). The hacky way, unfortunately, only supports basic kernels and mean functions, i.e. no kernel operations (such as sum or multiplication) allowed (for now).
-* once `GPFlow` 2.0 is out there and supports saving, this package will be updated accordingly
 
 ## Final notes
 When you encounter a bug or have any idea for an improvement, please open an issue and/or contact me.

diff --git a/examples/0-basic-optimisation.ipynb b/examples/0-basic-optimisation.ipynb
diff --git a/examples/1-callbacks.ipynb b/examples/1-callbacks.ipynb
diff --git a/examples/2-saving-model-output.ipynb b/examples/2-saving-model-output.ipynb
diff --git a/examples/3-saving-resuming-optimisation.ipynb b/examples/3-saving-resuming-optimisation.ipynb
diff --git a/requirements.txt b/requirements.txt
@@ -8,6 +8,5 @@ matplotlib
 flake8
 pytest
 black
-gast==0.2.2  # tensorflow 2.1.0 explicitely needs gast 0.2.2
 tensorflow>=2.1.0
-git+https://github.com/GPflow/GPflow.git@develop#egg=gpflow
+gpflow>=2.0.0
diff --git a/setup.py b/setup.py
@@ -1,4 +1,3 @@
-import re
 from os import path
 
 import setuptools
@@ -10,14 +9,6 @@
 with open("requirements.txt") as f:
     requirements = f.read().splitlines()
 
-checked_requirements = []
-for requirement in requirements:
-    if requirement.startswith("git+"):
-        # find package name from git address
-        pkg_name = re.findall(r"\/([a-zA-Z]*)\.git", requirement)[0]
-        requirement = f"{pkg_name.lower()} @ " + requirement
-    checked_requirements.append(requirement)
-
 extra_requirements = {}
 with open("requirements_optional.txt") as f:
     extra_reqs = f.read().splitlines()
@@ -27,7 +18,7 @@
 
 setuptools.setup(
     name="pygpso",
-    version="0.4",
+    version="0.4.1",
     description="Bayesian optimisation method leveraging Gaussian Processes "
     "surrogate",
     long_description=long_description,
@@ -47,7 +38,7 @@
         "Topic :: Scientific/Engineering :: Medical Science Apps.",
     ],
     python_requires=">=3.6",
-    install_requires=checked_requirements,
+    install_requires=requirements,
     extras_require=extra_requirements,
     include_package_data=True,
 )
diff --git a/tests/test_callbacks.py b/tests/test_callbacks.py
@@ -39,6 +39,9 @@ def test_init(self):
 
 
 class TestCallbacks(unittest.TestCase):
+    _ = pytest.importorskip("igraph")
+    _ = pytest.importorskip("pandas")
+    _ = pytest.importorskip("tables")
     callbacks = [
         PostIterationPlotting(
             filename_pattern=os.path.join(