Rename TNS into NeuroTS

.auto-changelog

@@ -0,0 +1,12 @@
+{
+    "output": "CHANGELOG.md",
+    "template": ".auto-changelog-template.hbs",
+    "commitLimit": false,
+    "backfillLimit": false,
+    "ignoreCommitPattern": "Release [0-9]+\\.[0-9]+\\.[0-9]+|Update CHANGELOG.*|.*\\[skip-changelog\\].*",
+    "commitUrl": "https://bbpgitlab.epfl.ch/neuromath/neurots/commit/{id}",
+    "issueUrl": "https://bbpgitlab.epfl.ch/neuromath/neurots/issues/{id}",
+    "mergeUrl": "https://bbpgitlab.epfl.ch/neuromath/neurots/merge_requests/{id}",
+    "compareUrl": "https://bbpgitlab.epfl.ch/neuromath/neurots/compare/{from}...{to}",
+    "tagPrefix": "NeuroTS-v"
+}

.auto-changelog-template.hbs

@@ -0,0 +1,31 @@
+# Changelog
+
+{{#each releases}}
+  {{#if href}}
+    ## [{{title}}]({{href}})
+  {{else}}
+    ## {{title}}
+  {{/if}}
+
+  {{#if tag}}
+    > {{niceDate}}
+  {{/if}}
+
+  {{#if summary}}
+    {{summary}}
+  {{/if}}
+
+  {{#each merges}}
+    - {{#if commit.breaking}}**Breaking change:** {{/if}}{{message}}{{#if href}} [#{{id}}]({{href}}){{/if}}
+  {{/each}}
+  {{#each fixes}}
+    - {{#if commit.breaking}}**Breaking change:** {{/if}}{{commit.subject}}{{#each fixes}} ({{author}}{{#if href}} - [#{{id}}]({{href}}){{/if}}){{/each}}
+  {{/each}}
+  {{#each commits}}
+    - {{#if breaking}}**Breaking change:** {{/if}}{{subject}} ({{author}}{{#if href}} - [{{shorthash}}]({{href}}){{/if}})
+  {{/each}}
+
+{{/each}}
+
+
+Generated by [auto-changelog](https://github.com/CookPete/auto-changelog).

.gitignore

@@ -10,11 +10,15 @@
 # Mac related stuff
 .DS_Store
 
+# Packaging builds
+build/
+dist/
+
 # tox
 .tox/
 
 # coverage
-.coverage
+.coverage*
 coverage.xml
 
 # test venv

.gitlab-ci.yml

@@ -0,0 +1,20 @@
+include:
+   - project: nse/ci
+     file:
+        - /ci/lib/tox-docker.yml
+        - /ci/jobs/check-version.yml
+        - /ci/jobs/check-packaging.yml
+        - /ci/jobs/lint.yml
+        - /ci/jobs/docs.yml
+        - /ci/jobs/build-package.yml
+        - /ci/jobs/publish-package.yml
+        - /ci/jobs/publish-docs.yml
+        - /ci/jobs/tag.yml
+   - project: neuromath/ci
+     file:
+        - /ci/jobs/auto-release.yml
+        - /ci/lib/pytest-template.yml
+        - /ci/jobs/py36.yml
+        - /ci/jobs/py37.yml
+        - /ci/jobs/py38.yml
+        - /ci/jobs/coverage.yml

README.rst

@@ -1,17 +1,13 @@
-Module: Topological Neuron Synthesis
-====================================
+Topological Neuron Synthesis
+============================
 
-Generation of artificial neuronal trees based on the topology of biological cells
-and their statistical properties
+Generation of artificial neuronal trees based on the topology of biological cells and their
+statistical properties.
 
 
 Installation instructions
 -------------------------
 
 .. code:: bash
 
-    virtualenv test_syn
-    source ./test_syn/bin/activate
-    git clone ssh://bbpcode.epfl.ch/molecularsystems/TNS
-    pip install --upgrade pip
-    pip install ./TNS --index-url  https://bbpteam.epfl.ch/repository/devpi/bbprelman/dev/+simple/
+    pip install --index-url https://bbpteam.epfl.ch/repository/devpi/bbprelman/dev/+simple/ tns

doc/Makefile

@@ -12,9 +12,13 @@ BUILDDIR      = build
 help:
 	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-.PHONY: help Makefile
+.PHONY: help Makefile clean
 
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
+	# Generate the documentation
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+clean:
+	@rm -rf $(SOURCEDIR)/generated $(BUILDDIR)

doc/source/api.rst

@@ -5,4 +5,4 @@ API Documentation
     :toctree: generated
     :recursive:
 
-    tns
+    neurots

doc/source/changelog.rst

@@ -1 +1 @@
-.. include:: ../../CHANGELOG.rst
+.. mdinclude:: ../../CHANGELOG.md

doc/source/conf.py

@@ -9,18 +9,18 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
+import os
+import sys
 from pkg_resources import get_distribution
 
+sys.path.insert(0, os.path.abspath('../..'))
+
 # -- Project information -----------------------------------------------------
 
-project = "TNS"
+project = "NeuroTS"
 
 # The short X.Y version
-version = get_distribution("tns").version
+version = get_distribution("neurots").version
 
 # The full version, including alpha/beta/rc tags
 release = version
@@ -34,10 +34,10 @@
 extensions = [
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
-    "sphinx.ext.graphviz",
-    "sphinx.ext.napoleon",
     "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
     "sphinx-jsonschema",
+    "m2r2",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -62,10 +62,10 @@
 # html_static_path = ['_static']
 
 html_theme_options = {
-    "metadata_distribution": "TNS",
+    "metadata_distribution": "NeuroTS",
 }
 
-html_title = "TNS"
+html_title = "NeuroTS"
 
 # If true, links to the reST sources are added to the pages.
 html_show_sourcelink = False
@@ -75,7 +75,11 @@
 
 # autodoc settings
 autodoc_typehints = "signature"
-autodoc_default_options = {"members": True, "show-inheritance": True, "special-members": "__init__"}
+autodoc_default_options = {
+    "members": True,
+    "show-inheritance": True,
+    "special-members": "__init__",
+}
 
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),

doc/source/index.rst

@@ -7,5 +7,5 @@
 
    Home <self>
    params_and_distrs
-   changelog
    api
+   changelog

doc/source/params_and_distrs.rst

@@ -1,12 +1,12 @@
 Parameters and distributions
 ============================
 
-This page describes the format of the expected parameters and distributions used by TNS.
+This page describes the format of the expected parameters and distributions used by NeuroTS.
 
 Parameters
 ----------
 
-.. jsonschema:: ../../tns/schemas/parameters.json
+.. jsonschema:: ../../neurots/schemas/parameters.json
     :lift_definitions:
     :auto_reference:
     :auto_target:
@@ -15,7 +15,7 @@ Parameters
 Distributions
 -------------
 
-.. jsonschema:: ../../tns/schemas/distributions.json
+.. jsonschema:: ../../neurots/schemas/distributions.json
     :lift_definitions:
     :auto_reference:
     :auto_target:

examples/fix_diameters.py

@@ -1,5 +1,5 @@
 import os
-import tns
+import neurots
 
 
 def run():
@@ -12,11 +12,11 @@ def run():
 
     # Generate model from input cell
 
-    model = tns.extract_input.diameter_distributions(input_cell)
+    model = neurots.extract_input.diameter_distributions(input_cell)
 
     # Create the object to modify the input cell to be diametrized
     # Initialize tha cell with the output cell name
-    G = tns.NeuronGrower(input_parameters=None, input_distributions=model, name=output_cell_name)
+    G = neurots.NeuronGrower(input_parameters=None, input_distributions=model, name=output_cell_name)
 
     # Modify the diameters using the generated model
     G.diametrize()

examples/generate_cell.py

@@ -1,6 +1,6 @@
 import os
-import tns
-from tns import extract_input
+import neurots
+from neurots import extract_input
 def run():
     # Extract distributions from cells in input directory
     dir_path = os.path.dirname(os.path.realpath(__file__))
@@ -11,7 +11,7 @@ def run():
                                           feature='path_distances', method='tmd', diameter_parameters='M5')
 
     # Initialize a neuron
-    N = tns.NeuronGrower(input_distributions=distr,
+    N = neurots.NeuronGrower(input_distributions=distr,
                          input_parameters=params)
 
     # Grow your neuron