From a44566ef08d97a7f253ea5af8ea0f728f51e24ba Mon Sep 17 00:00:00 2001
From: Michele Fabbri <michele.fabbri@internationalbrainlab.org>
Date: Tue, 24 May 2022 13:08:41 +0100
Subject: [PATCH 1/4] init ci

---
 .flake8                  |  2 +-
 .github/workflows/ci.yml | 41 ++++++++++++++++++++++++++++++++++++++++
 .gitignore               |  3 +++
 .travis.yml              | 25 ------------------------
 requirements.txt         |  2 +-
 5 files changed, 46 insertions(+), 27 deletions(-)
 create mode 100644 .github/workflows/ci.yml
 delete mode 100644 .travis.yml

diff --git a/.flake8 b/.flake8
index 9ebe579..8689cb4 100644
--- a/.flake8
+++ b/.flake8
@@ -1,5 +1,5 @@
 [flake8]
-max-line-length = 99
+max-line-length = 130
 ignore = W504
 exclude =
     .git,
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..ea09a70
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,41 @@
+name: CI
+
+on:
+  push:
+    branches: [ master, develop, ci_and_pypi ] # TODO: remove additional branch when deploying to production
+  pull_request:
+    branches: [ master, develop ]
+
+jobs:
+  build:
+    name: build (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      max-parallel: 3
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+        python-version: ["3.8", "3.9"]
+    steps:
+    - name: Clone repo
+      uses: actions/checkout@v3
+      with:
+        ref: ci_and_pypi  # TODO: remove when deploying to master
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install deps
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        pip install -r requirements.txt
+        pip install -e .
+    # TODO: enable flake8 and tests when we have a better handle on what is important
+#    - name: Flake8
+#      run: |
+#        python -m flake8
+#    - name: Tests
+#      run: |
+#        cd tests
+#        python -m unittest discover
diff --git a/.gitignore b/.gitignore
index 7640b7a..438dc89 100644
--- a/.gitignore
+++ b/.gitignore
@@ -135,3 +135,6 @@ dmypy.json
 .vscode/
 
 scratch/
+
+# pycharm
+.idea/*
\ No newline at end of file
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 6324eff..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,25 +0,0 @@
-language: python
-python:
-  - "3.7"
-# command to install dependencies
-install:
-  - pip install -r requirements.txt
-  - pip install -e .
-  # install develop branch of ibllib
-  - pip install git+https://github.com/int-brain-lab/ibllib.git@develop
-
- # command to run tests
-before_script:
-  - echo "exec('from oneibl.one import ONE; ONE(silent=True)')" | python
-  - sed -i 's|null|"'$IBLFLATIRONPASS'"|g' /home/travis/.one_params
-  # command to run tests
-
-script:
-  - bash ./run_tests
-  - flake8 .
-
-# only build master and develop (PRs are built for all branches)
-branches:
-  only:
-  - master
-  - develop
diff --git a/requirements.txt b/requirements.txt
index f5cbdcb..eabf653 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 easyqc
 ibllib
+PyQt5
 pyqtgraph
 simpleITK
-PyQt5

From 2277700a3d1037b913831ca0975f6feb412a6ad9 Mon Sep 17 00:00:00 2001
From: Michele Fabbri <michele.fabbri@internationalbrainlab.org>
Date: Tue, 24 May 2022 13:52:47 +0100
Subject: [PATCH 2/4] init pypi

---
 .github/workflows/pypi.yml | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 .github/workflows/pypi.yml

diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml
new file mode 100644
index 0000000..bb94b4f
--- /dev/null
+++ b/.github/workflows/pypi.yml
@@ -0,0 +1,33 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

From 4e7195094ea24cfcc536c1ea432966e6a7357032 Mon Sep 17 00:00:00 2001
From: Michele Fabbri <michele.fabbri@internationalbrainlab.org>
Date: Tue, 24 May 2022 16:21:49 +0100
Subject: [PATCH 3/4] setup for pypi template

---
 __init__.py |  1 +
 setup.py    | 58 ++++++++++++++++++++++++++++++++++++++++++++++-------
 2 files changed, 52 insertions(+), 7 deletions(-)

diff --git a/__init__.py b/__init__.py
index e69de29..b3c06d4 100644
--- a/__init__.py
+++ b/__init__.py
@@ -0,0 +1 @@
+__version__ = "0.0.1"
\ No newline at end of file
diff --git a/setup.py b/setup.py
index ef3f9ee..1e14487 100644
--- a/setup.py
+++ b/setup.py
@@ -1,12 +1,56 @@
-from setuptools import setup, find_packages
+import sys
+from pathlib import Path
+
+from setuptools import find_packages, setup
+
+CURRENT_DIRECTORY = Path(__file__).parent.absolute()
+CURRENT_PYTHON = sys.version_info[:2]
+REQUIRED_PYTHON = (3, 8)
+VER_ERR_MSG = """
+==========================
+Unsupported Python version
+==========================
+This version of ibllib requires Python {}.{}, but you're trying to install it on Python {}.{}.
+"""
+if CURRENT_PYTHON < REQUIRED_PYTHON:
+    sys.stderr.write(VER_ERR_MSG.format(*REQUIRED_PYTHON + CURRENT_PYTHON))
+    sys.exit(1)
+
+with open("README.md", "r") as f:
+    long_description = f.read()
+
+with open("requirements.txt") as f:
+    require = [x.strip() for x in f.readlines() if not x.startswith("git+")]
+
+
+def read(rel_path):
+    here = Path(__file__).parent.absolute()
+    with open(here.joinpath(rel_path), "r") as fp:
+        return fp.read()
+
+
+def get_version(rel_path):
+    for line in read(rel_path).splitlines():
+        if line.startswith("__version__"):
+            delim = '"' if '"' in line else "'"
+            return line.split(delim)[1]
+    else:
+        raise RuntimeError("Unable to find version string.")
 
-with open('requirements.txt') as f:
-    require = [x.strip() for x in f.readlines() if not x.startswith('git+')]
 
 setup(
-    name='iblapps',
-    version='0.1',
-    packages=find_packages(),
+    name="iblapps",
+    version=get_version("__init__.py"),
+    python_requires=">={}.{}".format(*REQUIRED_PYTHON),
+    description="IBL Applications",
+    license="MIT",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    author="IBL Staff",
+    url="https://www.internationalbrainlab.com/",
+    packages=find_packages(exclude=["scratch"]),  # same as name
     include_package_data=True,
-    install_requires=require
+    # external packages as dependencies
+    install_requires=require,
+    scripts=[],
 )

From 7f0ae9d114b85895b40af22f4f3abbd4a25e18f0 Mon Sep 17 00:00:00 2001
From: Michele Fabbri <michele.fabbri@internationalbrainlab.org>
Date: Mon, 30 May 2022 15:55:26 +0100
Subject: [PATCH 4/4] minor changes for testing pypi

---
 .flake8          | 1 -
 requirements.txt | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/.flake8 b/.flake8
index 8689cb4..1182c13 100644
--- a/.flake8
+++ b/.flake8
@@ -1,6 +1,5 @@
 [flake8]
 max-line-length = 130
-ignore = W504
 exclude =
     .git,
     __pycache__,
diff --git a/requirements.txt b/requirements.txt
index eabf653..80b5c34 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,5 @@
 easyqc
+flake8
 ibllib
 PyQt5
 pyqtgraph