.github/stale.yml

@@ -0,0 +1,19 @@
+# Number of days of inactivity before an issue becomes stale
+daysUntilStale: 180 
+# Number of days of inactivity before a stale issue is closed
+daysUntilClose: 30 
+# Issues with these labels will never be considered stale
+exemptLabels:
+  - pinned
+  - bug
+  - feature-request
+  - security
+# Label to use when marking an issue as stale
+staleLabel: wontfix
+# Comment to post when marking an issue as stale. Set to `false` to disable
+markComment: >
+  This issue has been automatically marked as stale because it has not had
+  recent activity. It will be closed if no further activity occurs. Thank you
+  for your contributions.
+# Comment to post when closing a stale issue. Set to `false` to disable
+closeComment: false

.gitignore

@@ -11,6 +11,7 @@ build*
 *.egg-info
 *.so
 /temp
+/tmp
 /target
 __pycache__
 /pylint/pylint_*.txt
@@ -34,3 +35,6 @@ pyemma/setup.cfg
 
 # generated c-files:
 pyemma/_ext/variational/estimators/covar_c/covartools.c
+
+# pytest
+.pytest_cache

.gitmodules

@@ -1,4 +1,6 @@
-[submodule "ipython"]
-	path = pyemma-ipython
+[submodule "doc/source/legacy-notebooks"]
+	path = doc/source/legacy-notebooks
 	url = https://github.com/markovmodel/PyEMMA_IPython.git
-
+[submodule "doc/source/tutorials"]
+	path = doc/source/tutorials
+	url = https://github.com/markovmodel/pyemma_tutorials

.travis.yml

@@ -1,7 +1,7 @@
-language: c 
+language: c
 git:
   submodules: false
-  depth: 250
+  depth: 500
 os:
  - osx
  - linux
@@ -10,29 +10,47 @@ sudo: false
 
 env:
   global:
-    - PATH=$HOME/miniconda/bin:$PATH
-    - common_py_deps="conda-build=2.1.4"
-    - PACKAGENAME=pyemma
-    - ORGNAME=omnia
+    - MINICONDA_DIR="$HOME/miniconda"
     - PYTHONHASHSEED=0
     - OMP_NUM_THREADS=2
+    - PYEMMA_NJOBS=1
     - MACOSX_DEPLOYMENT_TARGET=10.9
+    - CONDA_BUILD=YES
   matrix:
-    - CONDA_PY=2.7 CONDA_NPY=1.11
-    - CONDA_PY=3.4 CONDA_NPY=1.10
-    - CONDA_PY=3.5 CONDA_NPY=1.11
-    - CONDA_PY=3.6 CONDA_NPY=1.11
+    - CONDA_PY='3.6'
+      CONDA_NPY='1.16'
+    - CONDA_PY='3.7'
+      CONDA_NPY='1.17'
+    - CONDA_PY='3.8'
+      CONDA_NPY='1.17'
+
+matrix:
+  exclude:  # test only 3.8 on osx.
+    - env: CONDA_PY=3.6
+      os: osx
+  include:  # test pip install
+    - env: CONDA_PY=3.7 CONDA_BUILD=NO python="3.7"
+      os: linux
+      dist: bionic # You’ll need to add dist: bionic to use Python 3.7 and higher.
+      language: python
+      sudo: true
+
 
 before_install:
-- devtools/ci/travis/install_miniconda.sh
-- conda config --set always_yes true
-- conda config --add channels omnia
-  #- conda config --add channels conda-forge
-- conda install -q $common_py_deps
+- if [[ ${CONDA_BUILD} = YES ]]; then
+    source devtools/ci/travis/install_miniconda.sh;
+  fi
 
 script:
-- conda build -q devtools/conda-recipe
+  - if [[ ${CONDA_BUILD} = YES ]]; then
+      conda build -q devtools/conda-recipe -c conda-forge;
+    else
+      pip install pip -U;
+      pip install . ;
+      rm -r pyemma;
+      pip install pytest tables;
+      pytest --pyargs pyemma;
+    fi
 
 after_script:
-- bash <(curl -s https://codecov.io/bash) -f $HOME/coverage.xml -e CONDA_PY,CONDA_NPY
-
+-  if [[ ${CONDA_BUILD} = YES ]]; then bash <(curl -s https://codecov.io/bash) -f $HOME/coverage.xml -e CONDA_PY; fi

AUTHORS

@@ -22,3 +22,11 @@ John Chodera
 Josh Fass
 Stephan Doerr
 @vargaslo
+Simon Olsson
+Brooke Husic
+Tim Hempel
+Sander Roet
+Sebastian Falkner
+Finn Krein
+Wei-Tse Hsu
+Côme Cattin

MANIFEST.in

@@ -1,15 +1,11 @@
 include README.rst
 include LICENSE.txt
+include pyproject.toml
 
 # include test modules in pyemma directory
-#recursive-include pyemma/msm/tests
-#recursive-include pyemma/msm/io/tests
-#recursive-include pyemma/msm/io/matrix/testfiles
-
 recursive-include pyemma tests/* tests/data/*
 recursive-include pyemma testfiles/*
 
-
 # exclude compiled bytecode
 global-exclude *.pyc
 # exclude git backup files
@@ -22,21 +18,23 @@ include pyemma/_version.py
 # setup stuff
 include setup_util.py
 
-# documentation
-graft doc
-prune doc/build
-prune doc/source/generated
-prune doc/source/api/generated
-
-# ipython notebooks
-#graft pyemma-ipython
-#recursive-exclude pyemma-ipython .ipynb_checkpoints
-
-# exclude git related files
-recursive-exclude * git .git*
-
 # sources of extensions (incl. cython)
 recursive-include pyemma *.pyx *.h *.c
 
 # do not include eventually present eggs (installed during setup runtime)
 prune .eggs
+
+recursive-include ext/pybind11/include *.h
+
+exclude pyemma/thermo/extensions/mbar/mbar.c \
+    pyemma/thermo/extensions/dtram/dtram.c \
+    pyemma/thermo/extensions/mbar_direct/mbar_direct.c \
+    pyemma/thermo/extensions/trammbar_direct/trammbar_direct.c \
+    pyemma/thermo/extensions/util/util.c \
+    pyemma/thermo/extensions/bar/bar.c \
+    pyemma/thermo/extensions/trammbar/trammbar.c \
+    pyemma/thermo/extensions/tram/tram.c \
+    pyemma/thermo/extensions/wham/wham.c \
+    pyemma/thermo/extensions/tram_direct/tram_direct.c \
+    pyemma/_ext/orderedset/_orderedset.c \
+    pyemma/_ext/variational/solvers/eig_qr/eig_qr.c \

README.rst

@@ -1,17 +1,21 @@
+=============================================
+This project is no longer actively maintained
+=============================================
+
+An alternative package reflecting most of PyEMMA's functionality is `deeptime <https://github.com/deeptime-ml/deeptime>`__.
+
 =====================================
 EMMA (Emma's Markov Model Algorithms)
 =====================================
 
-.. image:: https://img.shields.io/travis/markovmodel/PyEMMA/master.svg
-   :target: https://travis-ci.org/markovmodel/PyEMMA
+.. image:: https://img.shields.io/azure-devops/build/clonker/e16cf5d1-7827-4597-8bb5-b0f7577c73d1/6
+   :target: https://dev.azure.com/clonker/pyemma/_build
 .. image:: https://img.shields.io/pypi/v/pyemma.svg
    :target: https://pypi.python.org/pypi/pyemma
-.. image:: https://img.shields.io/pypi/dm/pyemma.svg
-   :target: https://pypi.python.org/pypi/pyemma
-.. image:: https://anaconda.org/omnia/pyemma/badges/downloads.svg
-   :target: https://anaconda.org/omnia/pyemma
-.. image:: https://anaconda.org/omnia/pyemma/badges/installer/conda.svg
-   :target: https://conda.anaconda.org/omnia
+.. image:: https://anaconda.org/conda-forge/pyemma/badges/downloads.svg
+   :target: https://anaconda.org/conda-forge/pyemma
+.. image:: https://anaconda.org/conda-forge/pyemma/badges/installer/conda.svg
+   :target: https://conda.anaconda.org/conda-forge
 .. image:: https://img.shields.io/codecov/c/github/markovmodel/PyEMMA/devel.svg
    :target: https://codecov.io/gh/markovmodel/PyEMMA/branch/devel
 
@@ -47,24 +51,28 @@ If you use PyEMMA in scientific work, please cite:
 
 Installation
 ------------
-With pip::
+If you want to use Miniconda on Linux or OSX, you can run this script to download and install everything::
 
-   pip install pyemma
+   curl -s https://raw.githubusercontent.com/markovmodel/PyEMMA/devel/install_miniconda%2Bpyemma.sh | bash
 
-with conda::
+If you have Anaconda/Miniconda installed, use the following::
 
-   conda install -c omnia pyemma
+   conda install -c conda-forge pyemma
+
+With pip::
+
+   pip install pyemma
 
 or install latest devel branch with pip::
 
    pip install git+https://github.com/markovmodel/PyEMMA.git@devel
 
-For a complete guide to installation, please have a look at the version 
+For a complete guide to installation, please have a look at the version
 `online <http://www.emma-project.org/latest/INSTALL.html>`__ or offline in file
 doc/source/INSTALL.rst
 
 To build the documentation offline you should install the requirements with::
-   
+
    pip install -r requirements-build-doc.txt
 
 Then build with make::
@@ -74,7 +82,7 @@ Then build with make::
 
 Support and development
 -----------------------
-For bug reports/suggestions/complaints please file an issue on 
+For bug reports/suggestions/complaints please file an issue on
 `GitHub <http://github.com/markovmodel/PyEMMA>`__.
 
 Or start a discussion on our mailing list: pyemma-users@lists.fu-berlin.de
@@ -83,6 +91,4 @@ Or start a discussion on our mailing list: pyemma-users@lists.fu-berlin.de
 External Libraries
 ------------------
 * mdtraj (LGPLv3): https://mdtraj.org
-* bhmm (LGPLv3): http://github.com/bhmm/bhmm
-* msmtools (LGLPv3): http://github.com/markovmodel/msmtools
 * thermotools (LGLPv3): http://github.com/markovmodel/thermotools

azure-pipelines.yml

@@ -0,0 +1,12 @@
+trigger:
+  - devel
+
+pr:
+  - devel
+
+stages:
+- stage: Test
+  jobs:
+  - template: ./devtools/azure-pipelines-linux.yml
+  - template: ./devtools/azure-pipelines-osx.yml
+  - template: ./devtools/azure-pipelines-win.yml