Change how deployment package is tracked so it can be deleted properly (

#31)

* Add docs Makefile

* Add placeholder files for deployment package

- Remove manifest.json from gitignore so Git will track the empty file
- Add empty placeholders for deployment package files and indicate these
  are package data so pip will remove the deployment files on uninstall

* Add check for empty files and indicator to download deployment package

* Fix code-style error

.gitignore

@@ -22,7 +22,6 @@ mylab.*.yaml
 *.npy
 *.nwb
 !/tests/back_compat/*.nwb
-manifest.json
 
 # Auto-generated tutorials
 docs/source/tutorials/
@@ -73,5 +72,5 @@ tests/coverage/htmlcov
 #mypy
 .mypy_cache/
 
-# trained model and taxonomy package
-src/gtnet/deploy_pkg/
+# sphinx autogen API docs
+docs/source/gtnet*.rst

docs/Makefile

@@ -0,0 +1,164 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS     =
+SPHINXBUILD    = sphinx-build
+SPHINXAPIDOC   = sphinx-apidoc
+PAPER          =
+BUILDDIR       = _build
+SRCDIR         = ../src
+RSTDIR         = source
+GALLERYDIR     = gallery
+PKGNAME        = hdmf
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) $(RSTDIR)
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@echo "  clean      to clean all documents built by Sphinx in _build"
+	@echo "  apidoc     to build RST from source code"
+
+clean:
+	-rm -rf $(BUILDDIR)/* $(RSTDIR)/$(PKGNAME)*.rst $(GALLERYDIR)/*.hdf5 $(GALLERYDIR)/*.sqlite $(RSTDIR)/tutorials
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/sample.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/sample.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/sample"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/sample"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+apidoc:
+	$(SPHINXAPIDOC) -f -e --no-toc -o $(RSTDIR) $(SRCDIR)
+	@echo "Build rst docs from source code."

pyproject.toml

@@ -45,6 +45,11 @@ dependencies = [
 ]
 dynamic = ["version"]
 
+[tool.setuptools.package-data]
+gtnet = ["deploy_pkg/*.npz",
+         "deploy_pkg/*.pt",
+         "deploy_pkg/manifest.json"]
+
 [project.urls]
 "Homepage" = "https://github.com/exabiome/gtnet"
 "Bug Tracker" = "https://github.com/exabiome/gtnet/issues"

src/gtnet/classify.py

@@ -55,7 +55,7 @@ def classify(argv=None):
     logger.info(f'Getting probability cutoffs for target false-positive rate of {args.fpr}')
     cutoffs = get_cutoffs(rocs, args.fpr)
 
-    logger.info(f'Filtering class predictions')
+    logger.info('Filtering class predictions')
     output = filter_predictions(output, cutoffs)
 
     write_csv(output, args)

src/gtnet/utils.py

@@ -1,3 +1,4 @@
+import glob
 import hashlib
 import json
 import logging
@@ -40,9 +41,12 @@ class DeployPkg:
     @classmethod
     def check_pkg(cls):
         deploy_dir = resource_filename(__name__, 'deploy_pkg')
-        if not os.path.exists(deploy_dir):
+        total = 0
+        for path in glob.glob(f"{deploy_dir}/*"):
+            total += os.path.getsize(path)
+        if total == 0:
             msg = ("Downloading GTNet deployment package. This will only happen on the first invocation "
-                   "of gtnet predict")
+                   "of gtnet predict or gtnet classify")
             warnings.warn(msg)
             zip_path = resource_filename(__name__, 'deploy_pkg.zip')
             urllib.request.urlretrieve(cls._deploy_pkg_url, zip_path)