--- a/env/lib/python3.7/site-packages/planemo/training/topic.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,218 +0,0 @@
-"""Module contains code for the Topic class, dealing with the creation of a training topic."""
-
-import collections
-import os
-
-from planemo import templates
-from .utils import (
-    load_yaml,
-    Requirement,
-    save_to_yaml
-)
-
-
-INDEX_FILE_TEMPLATE = """---
-layout: topic
-topic_name: {{ topic }}
----
-"""
-
-README_FILE_TEMPLATE = """
-{{ topic }}
-==========
-
-Please refer to the [CONTRIBUTING.md](../../CONTRIBUTING.md) before adding or updating any material
-"""
-
-
-DOCKER_FILE_TEMPLATE = """
-# Galaxy - {{ topic_title }}
-#
-# to build the docker image, go to root of training repo and
-#    docker build -t {{ topic_name }} -f topics/{{ topic_name }}/docker/Dockerfile .
-#
-# to run image:
-#    docker run -p "8080:80" -t {{ topic_name }}
-#    use -d to automatically dowload the datalibraries in the container
-
-FROM bgruening/galaxy-stable:latest
-
-MAINTAINER Galaxy Training Material
-
-ENV GALAXY_CONFIG_BRAND "GTN: {{ topic_title }}"
-
-# copy the tutorials directory for your topic
-ADD topics/{{ topic_name }}/tutorials/ /tutorials/
-
-# install everything for tutorials
-ADD bin/docker-install-tutorials.sh /setup-tutorials.sh
-ADD bin/mergeyaml.py /mergeyaml.py
-ADD bin/data_libarary_download.sh /data_libarary_download.sh
-RUN /setup-tutorials.sh
-
-ENTRYPOINT ["/data_libarary_download.sh"]
-"""
-
-
-INTRO_SLIDES_FILE_TEMPLATE = """---
-layout: introduction_slides
-logo: "GTN"
-
-title: {{ title }}
-type: {{ type }}
-contributors:
-- contributor
----
-
-### How to fill the slide decks?
-
-Please follow our
-[tutorial to learn how to fill the slides]({{ '{{' }} site.baseurl {{ '}}' }}/topics/contributing/tutorials/create-new-tutorial-slides/slides.html)
-"""
-
-
-class Topic(object):
-    """Class to describe a training topic."""
-
-    def __init__(self, name="new_topic", target="use", title="The new topic", summary="Summary", parent_dir="topics"):
-        """Init a topic instance."""
-        self.name = name
-        self.type = target
-        self.title = title
-        self.summary = summary
-        self.docker_image = ""
-        self.maintainers = ["maintainers"]
-        self.parent_dir = parent_dir
-        self.set_default_requirement()
-        self.set_paths()
-
-    def init_from_kwds(self, kwds):
-        """Init a topic instance from a kwds dictionary."""
-        self.name = kwds["topic_name"]
-        self.type = kwds["topic_target"]
-        self.title = kwds["topic_title"]
-        self.summary = kwds["topic_summary"]
-        self.set_default_requirement()
-        self.set_paths()
-
-    def init_from_metadata(self):
-        """Init a topic instance from the metadata file."""
-        metadata = load_yaml(self.metadata_fp)
-        self.name = metadata['name']
-        self.type = metadata['type']
-        self.title = metadata['title']
-        self.summary = metadata['summary']
-        self.requirements = []
-        if 'requirements' in metadata:
-            for r in metadata['requirements']:
-                req = Requirement()
-                req.init_from_dict(r)
-                self.requirements.append(req)
-        if 'docker_image' in metadata:
-            self.docker_image = metadata['docker_image']
-        self.maintainers = metadata['maintainers']
-        self.set_paths()
-
-    # GETTERS
-    def get_requirements(self):
-        """Get the requirements as a list of ordered dictionaries."""
-        reqs = []
-        for req in self.requirements:
-            reqs.append(req.export_to_ordered_dict())
-        return reqs
-
-    def export_metadata_to_ordered_dict(self):
-        """Export the topic metadata into an ordered dictionary."""
-        metadata = collections.OrderedDict()
-        metadata['name'] = self.name
-        metadata['type'] = self.type
-        metadata['title'] = self.title
-        metadata['summary'] = self.summary
-        metadata['requirements'] = self.get_requirements()
-        metadata['docker_image'] = self.docker_image
-        metadata['maintainers'] = self.maintainers
-        return metadata
-
-    # SETTERS
-    def set_default_requirement(self):
-        """Set default requirement: Galaxy introduction."""
-        self.requirements = []
-        if self.type == 'use':
-            self.requirements.append(Requirement())
-
-    def set_paths(self):
-        """Set the paths to folder and files."""
-        self.dir = os.path.join(self.parent_dir, self.name)
-        self.img_folder = os.path.join(self.dir, "images")
-        self.tuto_folder = os.path.join(self.dir, "tutorials")
-        self.index_fp = os.path.join(self.dir, "index.md")
-        self.readme_fp = os.path.join(self.dir, "README.md")
-        self.metadata_fp = os.path.join(self.dir, "metadata.yaml")
-        self.docker_folder = os.path.join(self.dir, "docker")
-        self.dockerfile_fp = os.path.join(self.docker_folder, "Dockerfile")
-        self.slides_folder = os.path.join(self.dir, "slides")
-
-    # TESTS
-    def exists(self):
-        """Test if the topic exists."""
-        return os.path.isdir(self.dir)
-
-    # OTHER METHODS
-    def create_topic_structure(self):
-        """Create the skeleton of a new topic.
-
-        1. create the folder and its structure
-        2. update the index.md to match your topic's name
-        3. fill the metadata
-        4. add a symbolic link to the metadata.yaml from the metadata folder
-        """
-        # create the folder and its structure
-        os.makedirs(self.dir)
-        self.img_folder = os.path.join(self.dir, "images")
-        os.makedirs(self.img_folder)
-        self.tuto_folder = os.path.join(self.dir, "tutorials")
-        os.makedirs(self.tuto_folder)
-
-        # create the index.md and add the topic name
-        self.index_fp = os.path.join(self.dir, "index.md")
-        with open(self.index_fp, 'w') as index_f:
-            index_f.write(
-                templates.render(INDEX_FILE_TEMPLATE, **{'topic': self.name}))
-
-        # create the README file
-        self.readme_fp = os.path.join(self.dir, "README.md")
-        with open(self.readme_fp, 'w') as readme_f:
-            readme_f.write(
-                templates.render(README_FILE_TEMPLATE, **{'topic': self.title}))
-
-        # create the metadata file
-        self.metadata_fp = os.path.join(self.dir, "metadata.yaml")
-        save_to_yaml(self.export_metadata_to_ordered_dict(), self.metadata_fp)
-
-        # create Dockerfile
-        self.docker_folder = os.path.join(self.dir, "docker")
-        os.makedirs(self.docker_folder)
-        self.dockerfile_fp = os.path.join(self.docker_folder, "Dockerfile")
-        with open(self.dockerfile_fp, 'w') as dockerfile:
-            dockerfile.write(
-                templates.render(
-                    DOCKER_FILE_TEMPLATE,
-                    **{'topic_name': self.name, 'topic_title': self.title}))
-
-        # create empty introduction slides
-        self.slides_folder = os.path.join(self.dir, "slides")
-        os.makedirs(self.slides_folder)
-        self.intro_slide_fp = os.path.join(self.slides_folder, "introduction.html")
-        with open(self.intro_slide_fp, 'w') as intro_slide_f:
-            intro_slide_f.write(
-                templates.render(
-                    INTRO_SLIDES_FILE_TEMPLATE,
-                    **{'title': "Introduction to %s" % self.title, 'type': "introduction"}))
-
-        # add a symbolic link to the metadata.yaml
-        metadata_dir = "metadata"
-        if not os.path.isdir(metadata_dir):
-            os.makedirs(metadata_dir)
-        os.chdir(metadata_dir)
-        os.symlink(os.path.join("..", self.metadata_fp), "%s.yaml" % self.name)
-        os.chdir("..")