Move to Torch (#7)

* move to torch

* remove pycharm folder

* remove pycharm folder try 2

* remove pycharm folder try 3

* Update README.md

* try travis matrix with python

.Rbuildignore

@@ -1,5 +1,20 @@
 ^LICENSE\.md$
+^README\.md$
+^\.travis.yml$
+
+# dirs
+^img$
+^bin$
+^tensorsem$
+^tensorsem\.egg-info$
+^example$
+
+# python files
+^\.idea/.*$
+^__pycache__$
+^setup.py$
+^venv$
+
+# R files
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^img.*$
-^\.travis\.yml$

.gitattributes

@@ -0,0 +1,2 @@
+# Auto detect text files and perform LF normalization
+* text=auto

.gitignore

@@ -1,4 +1,127 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
 .Rproj.user
-.Rhistory
-.RData
-.Ruserdata
+.idea/

.travis.yml

@@ -1,15 +1,17 @@
-language: r
-cache:
-  - packages
-  - $HOME/.cache/pip
-latex: false
-before_install:
-  - R -e 'install.packages("devtools")'
-  - R -e 'devtools::install_github("rstudio/tensorflow")'
-  - R -e 'tensorflow::install_tensorflow(version = "2.1.0")' > tf_install_log.txt
 matrix:
   include:
-    - os: linux
+    - language: r
+      latex: false
+      os: linux
       r: release
-    - os: linux
+    - language: r
+      latex: false
+      os: linux
       r: devel
+    - language: python
+      python: "3.6"
+      install:
+        - pip install torch==1.5.0+cpu -f https://download.pytorch.org/whl/torch_stable.html
+        - pip install pandas matplotlib
+        - pip install .
+      script: python example/tensorsem_example.py

DESCRIPTION

@@ -1,22 +1,15 @@
 Package: tensorsem
 Type: Package
-Title: Structural Equation Models using TensorFlow
-Version: 0.1.2
+Title: Estimate structural equation models using computation graphs
+Version: 1.0.0
 Author: Erik-Jan van Kesteren
 Maintainer: Erik-Jan van Kesteren <[email protected]>
-Description: Perform Structural Equation Modeling using a TensorFlow
-    session. 
+Description: Use lavaan code to create structural equation models, use torch to estimate them. 
+    This package provides the interface between lavaan and python.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.0.2
 Imports: 
-    tensorflow,
     reticulate,
-    lavaan,
-    R6,
-    progress,
-    stringr,
-    methods
-Suggests: 
-    testthat
+    lavaan
+RoxygenNote: 7.1.0

LICENSE.md

@@ -553,7 +553,7 @@ and each file should have at least the “copyright” line and a pointer to
 where the full notice is found.
 
     <one line to give the program's name and a brief idea of what it does.>
-    Copyright (C) 2019 Erik-Jan van Kesteren
+    Copyright (C) 2020 Erik-Jan van Kesteren
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -573,7 +573,7 @@ Also add information on how to contact you by electronic and paper mail.
 If the program does terminal interaction, make it output a short notice like this
 when it starts in an interactive mode:
 
-    tensorsem Copyright (C) 2019 Erik-Jan van Kesteren
+    lavtorch Copyright (C) 2020 Erik-Jan van Kesteren
     This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
     This is free software, and you are welcome to redistribute it
     under certain conditions; type 'show c' for details.

NAMESPACE

@@ -1,12 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-export(tf_sem)
-importFrom(R6,R6Class)
-importFrom(methods,new)
-importFrom(progress,progress_bar)
-importFrom(stats,cov)
-importFrom(stringr,str_pad)
-importFrom(stringr,str_trim)
-importFrom(tensorflow,shape)
-importFrom(tensorflow,tf)
-importFrom(utils,getFromNamespace)
+export(lav_mod_to_torch_opts)
+export(partable_from_torch)
+export(syntax_to_torch_opts)
+export(torch_opts_to_file)