chore: roadie quickstart

lazaratan · Feb 24, 2022 · 06d4bda · 06d4bda
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Showing 24 changed files with 55 additions and 343 deletions.
diff --git a/{{cookiecutter.repo_name}}/.gitignore → .gitignore b/{{cookiecutter.repo_name}}/.gitignore → .gitignore
diff --git a/{{cookiecutter.repo_name}}/.yapfignore → .yapfignore b/{{cookiecutter.repo_name}}/.yapfignore → .yapfignore
diff --git a/{{cookiecutter.repo_name}}/Dockerfile.test → Dockerfile.test b/{{cookiecutter.repo_name}}/Dockerfile.test → Dockerfile.test
diff --git a/{{cookiecutter.repo_name}}/MANIFEST.in → MANIFEST.in b/{{cookiecutter.repo_name}}/MANIFEST.in → MANIFEST.in
diff --git a/README.md b/README.md
@@ -1,9 +1,31 @@
-**Note: Do not attempt to use this directly unless you
-know what you are doing. The happy path is to let `roadie` interact with this
-template for you.**
-
-This is a template repository. It will be used by `roadie` to instantiate
-instances. We will make an initial commit on those repos with this boilerplate,
-so there is traceability as to the version of this template the repo was created
-with. This could be useful in figuring out later upgrades necessary to keep
-a repo up-to-date with compliance standards.
+# gflownet
+
+GFlowNet related training and environment code
+
+## Installation
+
+### PIP
+
+This package is installable via [Nexus](nexus.rxrx.io). You should configure your PIP using the instructions listed at
+[roadie: PIP Configuration](https://github.com/recursionpharma/roadie#pip-configuration). Then, execute the following:
+
+```bash
+pip install gflownet
+```
+
+### Conda
+
+You will need [anaconda cloud setup](https://github.com/recursionpharma/drug-discovery/wiki/Anaconda-Setup#setup-anaconda-cloud-locally)
+in order to access the Recursion conda packages. Once that is setup you can install this library like so:
+
+```
+conda config --add channels conda-forge
+conda config --add channels defaults
+conda config --add channels recursion
+conda install gflownet
+```
+
+## Developing
+
+Please refer to [Developing Python at Recursion](https://github.com/recursionpharma/roadie/blob/trunk/Developing.md)
+for all tasks related to development of this codebase.
diff --git a/{{cookiecutter.repo_name}}/VERSION → VERSION b/{{cookiecutter.repo_name}}/VERSION → VERSION
diff --git a/...cutter.repo_name}}/conda.recipe/meta.yaml → conda.recipe/meta.yaml b/...cutter.repo_name}}/conda.recipe/meta.yaml → conda.recipe/meta.yaml
@@ -1,14 +1,10 @@
-{# raw is for ignoring templating with cookiecutter, leaving it for use with conda-build #}
-{% raw -%}
+
 {% set data = load_setup_py_data() %}
-{%- endraw %}
 
 package:
-  name: {{cookiecutter.python_name}}
-  {# raw is for ignoring templating with cookiecutter, leaving it for use with conda-build #}
-  {% raw -%}
+  name: gflownet
+
   version: {{ data['version'] }}
-  {%- endraw %}
 
 source:
   path: ..
@@ -20,10 +16,6 @@ build:
   # "skip: True  # [not win]" to limit to Windows.
   script: python setup.py install --single-version-externally-managed --record=record.txt
   noarch: python
-  {%- if cookiecutter.cli == 'y' %}
-  entry_points:
-    - {{cookiecutter.python_name}} = {{cookiecutter.python_name}}.cli:cli
-  {%- endif %}
 
 requirements:
   build:
@@ -32,13 +24,11 @@ requirements:
     - roadie
   run:
     - python>=3.6
-    {% raw -%}
     # dependencies are defined in setup.py
     {% for dep in data['install_requires'] %}
     - {{ dep.lower() }}
     {% endfor %}
     {# raw is for ignoring templating with cookiecutter, leaving it for use with conda-build #}
-    {%- endraw %}
 
 test:
   source_files:
@@ -49,5 +39,5 @@ test:
     - pytest tests
 
 about:
-  home: https://github.com/recursionpharma/{{cookiecutter.repo_name}}
-  summary: {{cookiecutter.description}}
+  home: https://github.com/recursionpharma/gflownet
+  summary: GFlowNet related training and environment code
diff --git a/cookiecutter.json b/cookiecutter.json
diff --git a/{{cookiecutter.repo_name}}/tests/__init__.py → gflownet/__init__.py b/{{cookiecutter.repo_name}}/tests/__init__.py → gflownet/__init__.py
diff --git a/...me}}/{{cookiecutter.python_name}}/core.py → gflownet/core.py b/...me}}/{{cookiecutter.python_name}}/core.py → gflownet/core.py
@@ -1,5 +1,5 @@
 def get_version() -> str:
-    """Returns a string representation of the version of {{cookiecutter.python_name}} currently in use
+    """Returns a string representation of the version of gflownet currently in use
 
     Returns
     -------
@@ -8,11 +8,11 @@ def get_version() -> str:
     """
     try:
         from importlib.metadata import version  # type: ignore
-        return version('{{cookiecutter.python_name}}')
+        return version('gflownet')
     except ImportError:
         try:
             import pkg_resources
-            return pkg_resources.get_distribution('{{cookiecutter.python_name}}').version
+            return pkg_resources.get_distribution('gflownet').version
         except pkg_resources.DistributionNotFound:
             return 'set_version_placeholder'
     except ModuleNotFoundError:

diff --git a/hooks/post_gen_project.py b/hooks/post_gen_project.py
diff --git a/...kiecutter.repo_name}}/requirements/dev.in → requirements/dev.in b/...kiecutter.repo_name}}/requirements/dev.in → requirements/dev.in
diff --git a/...iecutter.repo_name}}/requirements/main.in → requirements/main.in b/...iecutter.repo_name}}/requirements/main.in → requirements/main.in
@@ -2,8 +2,4 @@
 # there are heavy things that only provide limited functionality consider adding
 # an optional extra package by including those dependencies in a separate file
 # in this directory with the .in extenion. Roadie will handle constructing your
-# package appropriately.
-
-{%- if cookiecutter.cli == 'y' %}
-click
-{%- endif %}
+# package appropriately.
diff --git a/{{cookiecutter.repo_name}}/setup.cfg → setup.cfg b/{{cookiecutter.repo_name}}/setup.cfg → setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
-name = {{cookiecutter.python_name}}
-description = {{cookiecutter.description}}
+name = gflownet
+description = GFlowNet related training and environment code
 url = https://github.com/recursionpharma/roadie
 version = set_version_placeholder
 author = Recursion Pharmaceuticals
@@ -9,16 +9,23 @@ classifiers =
 	Operating System :: OS Independent
 	Programming Language :: Python
 	Programming Language :: Python :: 3
-keywords = '{{cookiecutter.python_name}}'
+keywords = 'gflownet'
 
 [options]
 python_requires > = 3.6
 
 [flake8]
-{{cookiecutter.flake8}}
+max-line-length = 120
+exclude = build, tests, conda.recipe, benchmarks, .asv, .git, venv, migrations/versions, .tox
 
 [yapf]
-{{cookiecutter.yapf}}
+based_on_style = google
+allow_multiline_dictionary_keys = true
+allow_split_before_dict_value = false
+blank_line_before_nested_class_or_def = false
+coalesce_brackets = true
+column_limit = 120
+split_before_named_assigns = false
 
 [bdist_wheel]
 universal = True
@@ -29,9 +36,9 @@ addopts =
         -x
         --color=yes
         --cov-report term-missing
-        --cov={{cookiecutter.python_name}}
+        --cov=gflownet
 testpaths =
 	tests
 
 [mypy]
-files = {{cookiecutter.python_name}}
+files = gflownet
diff --git a/{{cookiecutter.repo_name}}/setup.py → setup.py b/{{cookiecutter.repo_name}}/setup.py → setup.py
@@ -8,7 +8,4 @@
     packages=find_packages(),
     install_requires=install_requires,
     extras_require=extras_require,
-  {%- if cookiecutter.cli == 'y' %}
-    entry_points={'console_scripts': ['{{cookiecutter.python_name}}={{cookiecutter.python_name}}.cli:cli']},
-  {%- endif %}
 )
diff --git a/template-tests/.gitignore b/template-tests/.gitignore
diff --git a/template-tests/requirements.txt b/template-tests/requirements.txt
diff --git a/template-tests/test.sh b/template-tests/test.sh
diff --git a/template-tests/test_generate.py b/template-tests/test_generate.py
diff --git a/.../{{cookiecutter.python_name}}/__init__.py → tests/__init__.py b/.../{{cookiecutter.python_name}}/__init__.py → tests/__init__.py
diff --git a/...okiecutter.repo_name}}/tests/test_core.py → tests/test_core.py b/...okiecutter.repo_name}}/tests/test_core.py → tests/test_core.py
@@ -1,4 +1,4 @@
-from {{cookiecutter.python_name}}.core import get_version
+from gflownet.core import get_version
 
 
 def test_get_version():

diff --git a/{{cookiecutter.repo_name}}/tox.ini → tox.ini b/{{cookiecutter.repo_name}}/tox.ini → tox.ini
diff --git a/{{cookiecutter.repo_name}}/README.md b/{{cookiecutter.repo_name}}/README.md