Merge branch 'pypi' into 'master'

Updates for pypi

See merge request algorithm/remora!86

.gitlab-ci.yml

@@ -7,7 +7,8 @@ before_script:
    - python -m venv venv
    - source venv/bin/activate
    - pip install -U pip
-   - pip install .[data_prep,tests]
+   - pip install .[tests]
+   - pip install git+https://github.com/nanoporetech/taiyaki
 
 format:py36:
     image: python:3.6

README.rst

@@ -18,7 +18,7 @@ To install from github source for development, the following commands can be run
 ::
 
    git clone [email protected]:nanoporetech/remora.git
-   pip install -e remora/[data_prep,tests]
+   pip install -e remora/[tests]
 
 See help for any Remora command with the ``-h`` flag.
 
@@ -76,6 +76,8 @@ Data Preparation
 ****************
 
 Remora data preparation begins from Taiyaki mapped signal files generally produced from Megalodon containing modified base annotations.
+This requires installation of Taiyaki via ``pip install git+https://github.com/nanoporetech/taiyaki``.
+
 An example dataset might be pre-processed with the following commands.
 
 .. code-block:: bash

setup.cfg

@@ -4,7 +4,7 @@ version = attr: src.remora.__init__.__version__
 description = Nanopore methylation/modified base calling detached from basecalling
 license = ont_public_licence
 long-description = file: README.rst
-long-description-content-type = text/rst; charset=UTF-8; variant=GFM
+long-description-content-type = text/x-rst; charset=UTF-8; variant=GFM
 url = https://github.com/nanoporetech/remora
 # Change if running only on Windows, Mac or Linux (comma-separated)
 platforms = any
@@ -36,8 +36,6 @@ install_requires =
 * = **.onnx
 
 [options.extras_require]
-data_prep =
-    taiyaki @ git+https://github.com/nanoporetech/taiyaki
 tests =
     pytest
     pytest-cov