From 2e8c2727a38d66b2fe8ffa08e2e12e0da144570a Mon Sep 17 00:00:00 2001
From: Michael Gecht <gecht.m@gmail.com>
Date: Thu, 18 Oct 2018 17:29:11 +0200
Subject: [PATCH 1/5] Replace `mdsynthesis` with `datreant`

---
 .travis.yml                                 | 22 +++---
 DEVELOPER.rst                               |  2 +-
 docs/docs-requirements.txt                  |  2 +-
 mdbenchmark/analyze.py                      |  9 ++-
 mdbenchmark/generate.py                     |  6 +-
 mdbenchmark/mdengines/gromacs.py            |  1 -
 mdbenchmark/mdengines/namd.py               |  1 -
 mdbenchmark/mdengines/utils.py              |  9 +--
 mdbenchmark/migrations/__init__.py          |  0
 mdbenchmark/migrations/mds_to_dtr.py        | 74 +++++++++++++++++++++
 mdbenchmark/submit.py                       | 10 ++-
 mdbenchmark/tests/mdengines/test_gromacs.py |  6 +-
 mdbenchmark/tests/mdengines/test_namd.py    |  6 +-
 mdbenchmark/tests/mdengines/test_utils.py   |  6 +-
 mdbenchmark/tests/test_analyze.py           |  9 ++-
 mdbenchmark/tests/test_generate.py          | 13 ++--
 mdbenchmark/tests/test_utils.py             |  7 +-
 mdbenchmark/utils.py                        |  3 +-
 setup.py                                    |  2 +-
 19 files changed, 129 insertions(+), 59 deletions(-)
 create mode 100644 mdbenchmark/migrations/__init__.py
 create mode 100644 mdbenchmark/migrations/mds_to_dtr.py

diff --git a/.travis.yml b/.travis.yml
index 63d65b2d..8d2a9504 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,13 +9,13 @@ branches:
 cache:
   - pip: true
   - directories:
-    - $PIP_CACHE_DIR
+      - $PIP_CACHE_DIR
 
 env:
   global:
     - MAIN_CMD="pytest"
     - SETUP_CMD="mdbenchmark -v"
-    - CONDA_DEPENDENCIES="mdsynthesis jinja2 click pandas matplotlib xdg<2"
+    - CONDA_DEPENDENCIES="datreant jinja2 click==6.7 pandas matplotlib xdg<2"
     - CONDA_CHANNELS="conda-forge"
     - NUMPY_VERSION=stable
     - PIP_CACHE_DIR=$HOME/.cache/pip
@@ -30,11 +30,9 @@ jobs:
       env:
         - CODECOV="--cov mdbenchmark"
         - PYTEST_COV="pytest-cov codecov"
-    -
-      name: "Python 3.5"
+    - name: "Python 3.5"
       python: "3.5"
-    -
-      name: "Python 2.7"
+    - name: "Python 2.7"
       python: "2.7"
 
     - stage: "Linting and formatting"
@@ -43,26 +41,22 @@ jobs:
         - $UPGRADE_PIP
         - pip install black
       script: make reformat-check
-    -
-      name: "Linting with flake8"
+    - name: "Linting with flake8"
       install:
         - $UPGRADE_PIP
         - pip install flake8
       script: make flake8
-    -
-      name: "Sorting with isort"
+    - name: "Sorting with isort"
       install:
         - $UPGRADE_PIP
         - pip install isort
       script: make isort
-    -
-      name: "Lint reStructuredText"
+    - name: "Lint reStructuredText"
       install:
         - $UPGRADE_PIP
         - pip install restructuredtext_lint
       script: make rst-lint
-    -
-      name: "Try to build documentation"
+    - name: "Try to build documentation"
       install:
         - $UPGRADE_PIP
         - pip install . sphinx-click
diff --git a/DEVELOPER.rst b/DEVELOPER.rst
index 98fb6e81..ce013fda 100644
--- a/DEVELOPER.rst
+++ b/DEVELOPER.rst
@@ -20,7 +20,7 @@ Create a virtual environment
 
 If you are using ``conda``, you can easily create a `conda environment`_::
 
-    $ conda create -n benchmark -c conda-forge mdsynthesis click
+    $ conda create -n benchmark -c conda-forge python=3
     $ source activate benchmark
 
 Make sure to activate the environment, before trying to install the package.
diff --git a/docs/docs-requirements.txt b/docs/docs-requirements.txt
index 84734dd2..1fd1f2c5 100644
--- a/docs/docs-requirements.txt
+++ b/docs/docs-requirements.txt
@@ -4,7 +4,7 @@ python-Levenshtein==0.12.0
 matplotlib==2.2.3
 numpy==1.15.1
 pandas==0.23.4
-mdsynthesis==0.6.1
+datreant==1.0.2
 xdg==1.0.7
 jinja2==2.10
 -e .
diff --git a/mdbenchmark/analyze.py b/mdbenchmark/analyze.py
index 070ac246..489131f2 100644
--- a/mdbenchmark/analyze.py
+++ b/mdbenchmark/analyze.py
@@ -19,8 +19,8 @@
 # along with MDBenchmark.  If not, see <http://www.gnu.org/licenses/>.
 import click
 
+import datreant as dtr
 import matplotlib.pyplot as plt
-import mdsynthesis as mds
 import numpy as np
 import pandas as pd
 from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
@@ -29,6 +29,7 @@
 from . import console
 from .cli import cli
 from .mdengines import detect_md_engine, utils
+from .migrations import mds_to_dtr
 from .plot import plot_over_group
 from .utils import generate_output_name, DataFrameFromBundle, PrintDataFrame
 
@@ -79,7 +80,11 @@ def analyze(directory, plot, ncores, output_name):
     `--output-name` option and a custom filename. To plot the results use
     `mdbenchmark plot`.
     """
-    bundle = mds.discover(directory)
+
+    # Migrate from MDBenchmark<2 to MDBenchmark=>2
+    mds_to_dtr.migrate_to_datreant(directory)
+
+    bundle = dtr.discover(directory)
 
     df = DataFrameFromBundle(bundle)
 
diff --git a/mdbenchmark/generate.py b/mdbenchmark/generate.py
index 37ed0132..216c7c57 100644
--- a/mdbenchmark/generate.py
+++ b/mdbenchmark/generate.py
@@ -19,13 +19,13 @@
 # along with MDBenchmark.  If not, see <http://www.gnu.org/licenses/>.
 import click
 
-import datreant.core as dtr
-import mdsynthesis as mds
+import datreant as dtr
 import pandas as pd
+
 from . import console, mdengines, utils
 from .cli import cli
 from .mdengines.utils import write_benchmark
-from .utils import DataFrameFromBundle, ConsolidateDataFrame, PrintDataFrame
+from .utils import ConsolidateDataFrame, DataFrameFromBundle, PrintDataFrame
 
 NAMD_WARNING = (
     "NAMD support is experimental. "
diff --git a/mdbenchmark/mdengines/gromacs.py b/mdbenchmark/mdengines/gromacs.py
index f40a80e7..36b219e5 100644
--- a/mdbenchmark/mdengines/gromacs.py
+++ b/mdbenchmark/mdengines/gromacs.py
@@ -24,7 +24,6 @@
 from glob import glob
 from shutil import copyfile
 
-import mdsynthesis as mds
 import numpy as np
 
 from .. import console
diff --git a/mdbenchmark/mdengines/namd.py b/mdbenchmark/mdengines/namd.py
index 472b3c31..1aff908f 100644
--- a/mdbenchmark/mdengines/namd.py
+++ b/mdbenchmark/mdengines/namd.py
@@ -22,7 +22,6 @@
 from glob import glob
 from shutil import copyfile
 
-import mdsynthesis as mds
 import numpy as np
 
 from .. import console
diff --git a/mdbenchmark/mdengines/utils.py b/mdbenchmark/mdengines/utils.py
index 0fb506fb..552876bd 100644
--- a/mdbenchmark/mdengines/utils.py
+++ b/mdbenchmark/mdengines/utils.py
@@ -22,7 +22,7 @@
 from glob import glob
 from shutil import copyfile
 
-import mdsynthesis as mds
+import datreant as dtr
 import numpy as np
 
 from .. import console
@@ -135,7 +135,8 @@ def cleanup_before_restart(engine, sim):
     whitelist = [re.compile(fname) for fname in whitelist]
 
     files_found = []
-    for fname in sim.leaves:
+
+    for fname in sim.leaves():
         keep = False
         for wl in whitelist:
             if wl.match(str(fname)):
@@ -153,8 +154,8 @@ def write_benchmark(
     engine, base_directory, template, nodes, gpu, module, name, host, time
 ):
     """Generate a benchmark folder with the respective Sim object."""
-    # Create the `mds.Sim` object
-    sim = mds.Sim(base_directory["{}/".format(nodes)])
+    # Create the `dtr.Treant` object
+    sim = dtr.Treant(base_directory["{}/".format(nodes)])
 
     # Do MD engine specific things. Here we also format the name.
     name = engine.prepare_benchmark(name=name, sim=sim)
diff --git a/mdbenchmark/migrations/__init__.py b/mdbenchmark/migrations/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/mdbenchmark/migrations/mds_to_dtr.py b/mdbenchmark/migrations/mds_to_dtr.py
new file mode 100644
index 00000000..6eaa9744
--- /dev/null
+++ b/mdbenchmark/migrations/mds_to_dtr.py
@@ -0,0 +1,74 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
+#
+# MDBenchmark
+# Copyright (c) 2017-2018 The MDBenchmark development team and contributors
+# (see the file AUTHORS for the full list of names)
+#
+# MDBenchmark is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# MDBenchmark is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with MDBenchmark.  If not, see <http://www.gnu.org/licenses/>.
+import fnmatch
+import json
+import os
+from glob import glob
+
+import datreant as dtr
+
+from .. import console
+
+
+def search_mdsynthesis_sim_files(folder):
+    """Search for `Sim.*.json` files generated by `mdsynthesis`."""
+    bundles = []
+    for root, dirnames, filenames in os.walk(folder):
+        for filename in fnmatch.filter(filenames, "Sim*"):
+            bundles.append(os.path.join(root, filename))
+
+    return bundles
+
+
+def convert_to_datreant(bundles):
+    """Convert old `mdsynthesis` data structures to vanilla `datreant.
+
+    Converts old `Sim.[...].json` files used in MDSynthesis<1.0 to datreant>1.0
+    `.datreant` folders.
+    """
+    for bundle in bundles:
+        with open(bundle) as fh:
+            sim = json.load(fh)
+
+        folder = "/".join(bundle.split("/")[0:-1])
+        dtr.Treant(folder, categories=sim["categories"], tags=sim["tags"])
+
+        # We want to remove two files, both `Sim.*.json` and `.Sim.*.json.proxy`.
+        files_to_remove = [bundle, glob(os.path.join(folder, ".Sim*"))]
+        for file in files_to_remove:
+            # The proxy file will be a list.
+            # We try to split the globbing result, if we fail, we skip this loop.
+            if isinstance(file, list):
+                try:
+                    file = file[0]
+                except IndexError:
+                    continue
+            os.remove(file)
+
+
+def migrate_to_datreant(directory):
+    """Perform the `mdsynthesis` to `datreant` migration."""
+    bundles = search_mdsynthesis_sim_files(directory)
+    if bundles:
+        console.info("Converting old benchmark metadata to new format!")
+        convert_to_datreant(bundles)
+        console.info("Finished converting old benchmarks to new format!")
+
+    return
diff --git a/mdbenchmark/submit.py b/mdbenchmark/submit.py
index 2c0aff0e..e4ec2db6 100644
--- a/mdbenchmark/submit.py
+++ b/mdbenchmark/submit.py
@@ -23,7 +23,7 @@
 
 import click
 
-import mdsynthesis as mds
+import datreant as dtr
 import numpy as np
 import pandas as pd
 
@@ -31,7 +31,8 @@
 from .cli import cli
 from .mdengines import detect_md_engine
 from .mdengines.utils import cleanup_before_restart
-from .utils import DataFrameFromBundle, ConsolidateDataFrame, PrintDataFrame
+from .migrations import mds_to_dtr
+from .utils import ConsolidateDataFrame, DataFrameFromBundle, PrintDataFrame
 
 PATHS = os.environ["PATH"].split(":")
 BATCH_SYSTEMS = {"slurm": "sbatch", "sge": "qsub", "Loadleveler": "llsubmit"}
@@ -77,7 +78,10 @@ def submit(directory, force_restart, yes):
     Only runs benchmarks that were not already started. Can be overwritten with
     `--force`.
     """
-    bundle = mds.discover(directory)
+    # Migrate from MDBenchmark<2 to MDBenchmark=>2
+    mds_to_dtr.migrate_to_datreant(directory)
+
+    bundle = dtr.discover(directory)
 
     # Exit if no bundles were found in the current directory.
     if not bundle:
diff --git a/mdbenchmark/tests/mdengines/test_gromacs.py b/mdbenchmark/tests/mdengines/test_gromacs.py
index 9f9b5a28..5c441990 100644
--- a/mdbenchmark/tests/mdengines/test_gromacs.py
+++ b/mdbenchmark/tests/mdengines/test_gromacs.py
@@ -17,11 +17,11 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with MDBenchmark.  If not, see <http://www.gnu.org/licenses/>.
-import datreant.core as dtr
-import numpy as np
-import pytest
 from six.moves import StringIO
 
+import datreant as dtr
+import numpy as np
+import pytest
 from mdbenchmark.mdengines import gromacs, utils
 
 
diff --git a/mdbenchmark/tests/mdengines/test_namd.py b/mdbenchmark/tests/mdengines/test_namd.py
index 28af4139..82e91732 100644
--- a/mdbenchmark/tests/mdengines/test_namd.py
+++ b/mdbenchmark/tests/mdengines/test_namd.py
@@ -17,11 +17,11 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with MDBenchmark.  If not, see <http://www.gnu.org/licenses/>.
-import datreant.core as dtr
-import numpy as np
-import pytest
 from six.moves import StringIO
 
+import datreant as dtr
+import numpy as np
+import pytest
 from mdbenchmark.mdengines import namd, utils
 
 
diff --git a/mdbenchmark/tests/mdengines/test_utils.py b/mdbenchmark/tests/mdengines/test_utils.py
index 5de18c23..d0ba896c 100644
--- a/mdbenchmark/tests/mdengines/test_utils.py
+++ b/mdbenchmark/tests/mdengines/test_utils.py
@@ -20,10 +20,8 @@
 import os
 from glob import glob
 
-import datreant.core as dtr
-import mdsynthesis as mds
+import datreant as dtr
 import pytest
-
 from mdbenchmark.mdengines import gromacs, namd, utils
 from mdbenchmark.utils import retrieve_host_template
 
@@ -38,7 +36,7 @@ def test_prepare_benchmark(engine, input_name, extensions, tmpdir):
         for ext in extensions:
             open("md.{}".format(ext), "a").close()
 
-        sim = mds.Sim("./{}".format(engine))
+        sim = dtr.Treant("./{}".format(engine))
         name = engine.prepare_benchmark(input_name, sim=sim)
 
         assert name == "md"
diff --git a/mdbenchmark/tests/test_analyze.py b/mdbenchmark/tests/test_analyze.py
index 08c2dbed..c267ee27 100644
--- a/mdbenchmark/tests/test_analyze.py
+++ b/mdbenchmark/tests/test_analyze.py
@@ -19,9 +19,8 @@
 # along with MDBenchmark.  If not, see <http://www.gnu.org/licenses/>.
 import os
 
+import datreant as dtr
 import pandas as pd
-import datreant.core as dtr
-import mdsynthesis as mds
 from mdbenchmark.utils import PrintDataFrame, ConsolidateDataFrame, DataFrameFromBundle
 from mdbenchmark import cli
 from mdbenchmark.ext.click_test import cli_runner
@@ -73,7 +72,7 @@ def test_analyze_namd(cli_runner, tmpdir, data):
             cli.cli, ["analyze", "--directory={}".format(data["analyze-files-namd"])]
         )
 
-        bundle = mds.discover(data["analyze-files-namd"])
+        bundle = dtr.discover(data["analyze-files-namd"])
         df = DataFrameFromBundle(bundle)
         test_output = PrintDataFrame(df, False) + "\n"
 
@@ -92,7 +91,7 @@ def test_analyze_with_errors(cli_runner, tmpdir, data):
             ["analyze", "--directory={}".format(data["analyze-files-w-errors"])],
         )
 
-        bundle = mds.discover(data["analyze-files-w-errors"])
+        bundle = dtr.discover(data["analyze-files-w-errors"])
         df = DataFrameFromBundle(bundle)
         test_output = PrintDataFrame(df, False) + "\n"
 
@@ -111,7 +110,7 @@ def test_analyze_plot(cli_runner, tmpdir, data):
             ],
         )
 
-        bundle = mds.discover(data["analyze-files-gromacs"])
+        bundle = dtr.discover(data["analyze-files-gromacs"])
         df = DataFrameFromBundle(bundle)
         test_output = PrintDataFrame(df, False) + "\n"
 
diff --git a/mdbenchmark/tests/test_generate.py b/mdbenchmark/tests/test_generate.py
index a5fa2b5d..7d96431d 100644
--- a/mdbenchmark/tests/test_generate.py
+++ b/mdbenchmark/tests/test_generate.py
@@ -22,9 +22,8 @@
 import pytest
 import pandas as pd
 from click import exceptions
-import datreant.core as dtr
-import mdsynthesis as mds
 
+import datreant as dtr
 from mdbenchmark import cli
 from mdbenchmark.utils import DataFrameFromBundle, PrintDataFrame, ConsolidateDataFrame
 from mdbenchmark.ext.click_test import cli_runner
@@ -81,7 +80,7 @@ def _output(gpu=True, n_benchmarks=4, runtime=15):
 def generate_output_table():
     def _output(short=False):
         title = "Benchmark Summary:\n"
-        bundle = mds.discover()
+        bundle = dtr.discover()
         df = DataFrameFromBundle(bundle)
         if short:
             df = ConsolidateDataFrame(df)
@@ -365,7 +364,7 @@ def test_generate_odd_number_of_nodes(
 
         output1 = "Creating benchmark system for {} with GPUs.\n".format(module)
 
-        bundle = mds.discover()
+        bundle = dtr.discover()
         df = DataFrameFromBundle(bundle)
         df = ConsolidateDataFrame(df)
         test_output = "Benchmark Summary:\n" + PrintDataFrame(df, False) + "\n"
@@ -503,7 +502,7 @@ def test_generate_namd_experimental_warning(cli_runner, monkeypatch, tmpdir):
             "If you use the --gpu option make sure you use the GPU compatible NAMD module!\n"
             "Creating benchmark system for namd/123.\n"
         )
-        bundle = mds.discover()
+        bundle = dtr.discover()
         df = DataFrameFromBundle(bundle)
         df = ConsolidateDataFrame(df)
         test_output = "Benchmark Summary:\n" + PrintDataFrame(df, False) + "\n"
@@ -628,7 +627,7 @@ def test_generate_test_prompt_yes(cli_runner, tmpdir, generate_output):
             "WARNING Cannot locate modules available on this host. Not performing module name validation.\n"
             "Creating benchmark system for gromacs/2016 with GPUs.\n"
         )
-        bundle = mds.discover()
+        bundle = dtr.discover()
         df = DataFrameFromBundle(bundle)
         df = ConsolidateDataFrame(df)
         output2 = (
@@ -663,6 +662,6 @@ def test_generate_test_prompt_no(cli_runner, tmpdir, generate_output):
             input="n\n",
         )
 
-        bundle = mds.discover()
+        bundle = dtr.discover()
         assert result.exit_code == 1
         assert len(bundle) == 0
diff --git a/mdbenchmark/tests/test_utils.py b/mdbenchmark/tests/test_utils.py
index 8b379461..ea1d06e7 100644
--- a/mdbenchmark/tests/test_utils.py
+++ b/mdbenchmark/tests/test_utils.py
@@ -19,12 +19,11 @@
 # along with MDBenchmark.  If not, see <http://www.gnu.org/licenses/>.
 import os
 
+import datreant as dtr
 import jinja2
 import numpy as np
 import pandas as pd
 import tabulate
-import datreant.core as dtr
-import mdsynthesis as mds
 from numpy.testing import assert_equal
 from pandas.testing import assert_frame_equal
 
@@ -158,7 +157,7 @@ def test_DataFrameFromBundle(data):
        This is used in other tests, therefore everything is hard coded
        If changes are made to the layout type this should be changed here.
     """
-    bundle = mds.discover(data["analyze-files-gromacs"])
+    bundle = dtr.discover(data["analyze-files-gromacs"])
     test_output = utils.DataFrameFromBundle(bundle)
 
     expected_output = pd.read_csv(data["analyze-files-gromacs.csv"])
@@ -173,7 +172,7 @@ def test_ConsolidateDataFrame(data):
         This is used in other tests, therefore everyting is hard coded.
         If changes are made to the layout type this should be changed here.
     """
-    bundle = mds.discover(data["analyze-files-gromacs"])
+    bundle = dtr.discover(data["analyze-files-gromacs"])
     df = utils.DataFrameFromBundle(bundle)
     test_output = utils.ConsolidateDataFrame(df)
 
diff --git a/mdbenchmark/utils.py b/mdbenchmark/utils.py
index d19647c1..b7d53dbc 100644
--- a/mdbenchmark/utils.py
+++ b/mdbenchmark/utils.py
@@ -25,9 +25,8 @@
 from tabulate import tabulate
 
 import click
+import datreant as dtr
 import numpy as np
-import datreant.core as dtr
-import mdsynthesis as mds
 import pandas as pd
 import xdg
 from jinja2 import ChoiceLoader, Environment, FileSystemLoader, PackageLoader
diff --git a/setup.py b/setup.py
index 94a3e462..77650f92 100644
--- a/setup.py
+++ b/setup.py
@@ -71,7 +71,7 @@ def get_property(prop, project):
     packages=find_packages(),
     install_requires=[
         "numpy>=1.8",
-        "mdsynthesis==0.6.1",
+        "datreant>=1.0.0",
         "click==6.7",  # v7.0 introduced some changes that broke our tests.
         "jinja2",
         "pandas",

From 3ff4aad93c9cc1cefa24a8f6691c1556b020f2a2 Mon Sep 17 00:00:00 2001
From: Michael Gecht <gecht.m@gmail.com>
Date: Thu, 18 Oct 2018 17:35:42 +0200
Subject: [PATCH 2/5] Convert old `mdsynthesis` tests to new `datreant` format

---
 .../tests/data/analyze-files-gromacs/1/.datreant/categories.json | 1 +
 .../1/Sim.f2c3a7de-e167-419e-a8b6-2286f27f674c.json              | 1 -
 .../tests/data/analyze-files-gromacs/2/.datreant/categories.json | 1 +
 .../2/Sim.7c0db0de-70ce-4d55-b53b-d31c904f11cb.json              | 1 -
 .../tests/data/analyze-files-gromacs/3/.datreant/categories.json | 1 +
 .../3/Sim.b4ca19ea-a5ba-49be-8f27-aab19938d888.json              | 1 -
 .../tests/data/analyze-files-gromacs/4/.datreant/categories.json | 1 +
 .../4/Sim.059d59b5-c86c-4f50-9ff6-6a2061e26bf6.json              | 1 -
 .../tests/data/analyze-files-gromacs/5/.datreant/categories.json | 1 +
 .../5/Sim.07ec0ddb-602d-4717-8464-22fc7dd50388.json              | 1 -
 .../tests/data/analyze-files-namd/1/.datreant/categories.json    | 1 +
 .../1/Sim.59e83777-6ebb-493e-a478-7195a4261493.json              | 1 -
 .../tests/data/analyze-files-namd/2/.datreant/categories.json    | 1 +
 .../2/Sim.6b71a7b2-6a3c-4a5a-a740-f4d2f361c337.json              | 1 -
 .../data/analyze-files-w-errors/1/.datreant/categories.json      | 1 +
 .../1/Sim.f2c3a7de-e167-419e-a8b6-2286f27f674c.json              | 1 -
 .../data/analyze-files-w-errors/2/.datreant/categories.json      | 1 +
 .../2/Sim.7c0db0de-70ce-4d55-b53b-d31c904f11cb.json              | 1 -
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 30 files changed, 15 insertions(+), 15 deletions(-)
 create mode 100644 mdbenchmark/tests/data/analyze-files-gromacs/1/.datreant/categories.json
 delete mode 100644 mdbenchmark/tests/data/analyze-files-gromacs/1/Sim.f2c3a7de-e167-419e-a8b6-2286f27f674c.json
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 delete mode 100644 mdbenchmark/tests/data/analyze-files-gromacs/2/Sim.7c0db0de-70ce-4d55-b53b-d31c904f11cb.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-gromacs/3/.datreant/categories.json
 delete mode 100644 mdbenchmark/tests/data/analyze-files-gromacs/3/Sim.b4ca19ea-a5ba-49be-8f27-aab19938d888.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-gromacs/4/.datreant/categories.json
 delete mode 100644 mdbenchmark/tests/data/analyze-files-gromacs/4/Sim.059d59b5-c86c-4f50-9ff6-6a2061e26bf6.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-gromacs/5/.datreant/categories.json
 delete mode 100644 mdbenchmark/tests/data/analyze-files-gromacs/5/Sim.07ec0ddb-602d-4717-8464-22fc7dd50388.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-namd/1/.datreant/categories.json
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 create mode 100644 mdbenchmark/tests/data/analyze-files-namd/2/.datreant/categories.json
 delete mode 100644 mdbenchmark/tests/data/analyze-files-namd/2/Sim.6b71a7b2-6a3c-4a5a-a740-f4d2f361c337.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-w-errors/1/.datreant/categories.json
 delete mode 100644 mdbenchmark/tests/data/analyze-files-w-errors/1/Sim.f2c3a7de-e167-419e-a8b6-2286f27f674c.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-w-errors/2/.datreant/categories.json
 delete mode 100644 mdbenchmark/tests/data/analyze-files-w-errors/2/Sim.7c0db0de-70ce-4d55-b53b-d31c904f11cb.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-w-errors/3/.datreant/categories.json
 delete mode 100644 mdbenchmark/tests/data/analyze-files-w-errors/3/Sim.b4ca19ea-a5ba-49be-8f27-aab19938d888.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-w-errors/4/.datreant/categories.json
 delete mode 100644 mdbenchmark/tests/data/analyze-files-w-errors/4/Sim.059d59b5-c86c-4f50-9ff6-6a2061e26bf6.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-w-errors/5/.datreant/categories.json
 delete mode 100644 mdbenchmark/tests/data/analyze-files-w-errors/5/Sim.07ec0ddb-602d-4717-8464-22fc7dd50388.json
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 delete mode 100644 mdbenchmark/tests/data/analyze-files-w-errors/6/Sim.215509f9-67dd-43d6-b437-99423e68d2d2.json
 create mode 100644 mdbenchmark/tests/data/analyze-files-w-errors/7/.datreant/categories.json
 delete mode 100644 mdbenchmark/tests/data/analyze-files-w-errors/7/Sim.6a47b788-410a-4b9d-9ab3-9492593b8cae.json
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 delete mode 100644 mdbenchmark/tests/data/analyze-files-w-errors/8/Sim.dc08e3e4-a081-4bef-9ca1-1a9080669655.json

diff --git a/mdbenchmark/tests/data/analyze-files-gromacs/1/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-gromacs/1/.datreant/categories.json
new file mode 100644
index 00000000..6b1d0f77
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-gromacs/1/.datreant/categories.json
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-gromacs/1/Sim.f2c3a7de-e167-419e-a8b6-2286f27f674c.json b/mdbenchmark/tests/data/analyze-files-gromacs/1/Sim.f2c3a7de-e167-419e-a8b6-2286f27f674c.json
deleted file mode 100644
index 9866f10f..00000000
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@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-gromacs/2/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-gromacs/2/.datreant/categories.json
new file mode 100644
index 00000000..b2cca829
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@@ -0,0 +1 @@
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diff --git a/mdbenchmark/tests/data/analyze-files-gromacs/2/Sim.7c0db0de-70ce-4d55-b53b-d31c904f11cb.json b/mdbenchmark/tests/data/analyze-files-gromacs/2/Sim.7c0db0de-70ce-4d55-b53b-d31c904f11cb.json
deleted file mode 100644
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diff --git a/mdbenchmark/tests/data/analyze-files-gromacs/3/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-gromacs/3/.datreant/categories.json
new file mode 100644
index 00000000..5d9a394b
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@@ -0,0 +1 @@
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diff --git a/mdbenchmark/tests/data/analyze-files-gromacs/3/Sim.b4ca19ea-a5ba-49be-8f27-aab19938d888.json b/mdbenchmark/tests/data/analyze-files-gromacs/3/Sim.b4ca19ea-a5ba-49be-8f27-aab19938d888.json
deleted file mode 100644
index 7d9af132..00000000
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@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-gromacs/4/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-gromacs/4/.datreant/categories.json
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@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-gromacs/4/Sim.059d59b5-c86c-4f50-9ff6-6a2061e26bf6.json b/mdbenchmark/tests/data/analyze-files-gromacs/4/Sim.059d59b5-c86c-4f50-9ff6-6a2061e26bf6.json
deleted file mode 100644
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+++ /dev/null
@@ -1 +0,0 @@
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diff --git a/mdbenchmark/tests/data/analyze-files-gromacs/5/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-gromacs/5/.datreant/categories.json
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@@ -0,0 +1 @@
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diff --git a/mdbenchmark/tests/data/analyze-files-gromacs/5/Sim.07ec0ddb-602d-4717-8464-22fc7dd50388.json b/mdbenchmark/tests/data/analyze-files-gromacs/5/Sim.07ec0ddb-602d-4717-8464-22fc7dd50388.json
deleted file mode 100644
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diff --git a/mdbenchmark/tests/data/analyze-files-namd/1/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-namd/1/.datreant/categories.json
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@@ -0,0 +1 @@
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diff --git a/mdbenchmark/tests/data/analyze-files-namd/1/Sim.59e83777-6ebb-493e-a478-7195a4261493.json b/mdbenchmark/tests/data/analyze-files-namd/1/Sim.59e83777-6ebb-493e-a478-7195a4261493.json
deleted file mode 100644
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diff --git a/mdbenchmark/tests/data/analyze-files-namd/2/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-namd/2/.datreant/categories.json
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@@ -0,0 +1 @@
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diff --git a/mdbenchmark/tests/data/analyze-files-namd/2/Sim.6b71a7b2-6a3c-4a5a-a740-f4d2f361c337.json b/mdbenchmark/tests/data/analyze-files-namd/2/Sim.6b71a7b2-6a3c-4a5a-a740-f4d2f361c337.json
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diff --git a/mdbenchmark/tests/data/analyze-files-w-errors/1/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-w-errors/1/.datreant/categories.json
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diff --git a/mdbenchmark/tests/data/analyze-files-w-errors/2/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-w-errors/2/.datreant/categories.json
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diff --git a/mdbenchmark/tests/data/analyze-files-w-errors/2/Sim.7c0db0de-70ce-4d55-b53b-d31c904f11cb.json b/mdbenchmark/tests/data/analyze-files-w-errors/2/Sim.7c0db0de-70ce-4d55-b53b-d31c904f11cb.json
deleted file mode 100644
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+++ /dev/null
@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-w-errors/3/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-w-errors/3/.datreant/categories.json
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+++ /dev/null
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\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-w-errors/4/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-w-errors/4/.datreant/categories.json
new file mode 100644
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@@ -0,0 +1 @@
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deleted file mode 100644
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+++ /dev/null
@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-w-errors/5/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-w-errors/5/.datreant/categories.json
new file mode 100644
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\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-w-errors/5/Sim.07ec0ddb-602d-4717-8464-22fc7dd50388.json b/mdbenchmark/tests/data/analyze-files-w-errors/5/Sim.07ec0ddb-602d-4717-8464-22fc7dd50388.json
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--- a/mdbenchmark/tests/data/analyze-files-w-errors/5/Sim.07ec0ddb-602d-4717-8464-22fc7dd50388.json
+++ /dev/null
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\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-w-errors/6/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-w-errors/6/.datreant/categories.json
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@@ -0,0 +1 @@
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diff --git a/mdbenchmark/tests/data/analyze-files-w-errors/6/Sim.215509f9-67dd-43d6-b437-99423e68d2d2.json b/mdbenchmark/tests/data/analyze-files-w-errors/6/Sim.215509f9-67dd-43d6-b437-99423e68d2d2.json
deleted file mode 100644
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+++ /dev/null
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\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-w-errors/7/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-w-errors/7/.datreant/categories.json
new file mode 100644
index 00000000..096b6c2f
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@@ -0,0 +1 @@
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diff --git a/mdbenchmark/tests/data/analyze-files-w-errors/7/Sim.6a47b788-410a-4b9d-9ab3-9492593b8cae.json b/mdbenchmark/tests/data/analyze-files-w-errors/7/Sim.6a47b788-410a-4b9d-9ab3-9492593b8cae.json
deleted file mode 100644
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--- a/mdbenchmark/tests/data/analyze-files-w-errors/7/Sim.6a47b788-410a-4b9d-9ab3-9492593b8cae.json
+++ /dev/null
@@ -1 +0,0 @@
-{"mdsynthesis": {}, "categories": {"name": "bench", "started": true, "module": "gromacs/2016.3", "host": "draco", "time": 15, "gpu": false, "nodes": 7}, "tags": []}
\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-w-errors/8/.datreant/categories.json b/mdbenchmark/tests/data/analyze-files-w-errors/8/.datreant/categories.json
new file mode 100644
index 00000000..f45ece8d
--- /dev/null
+++ b/mdbenchmark/tests/data/analyze-files-w-errors/8/.datreant/categories.json
@@ -0,0 +1 @@
+{"name": "bench", "started": true, "module": "gromacs/2016.3", "host": "draco", "time": 15, "gpu": false, "nodes": 8}
\ No newline at end of file
diff --git a/mdbenchmark/tests/data/analyze-files-w-errors/8/Sim.dc08e3e4-a081-4bef-9ca1-1a9080669655.json b/mdbenchmark/tests/data/analyze-files-w-errors/8/Sim.dc08e3e4-a081-4bef-9ca1-1a9080669655.json
deleted file mode 100644
index 5801c595..00000000
--- a/mdbenchmark/tests/data/analyze-files-w-errors/8/Sim.dc08e3e4-a081-4bef-9ca1-1a9080669655.json
+++ /dev/null
@@ -1 +0,0 @@
-{"mdsynthesis": {}, "categories": {"name": "bench", "started": true, "module": "gromacs/2016.3", "host": "draco", "time": 15, "gpu": false, "nodes": 8}, "tags": []}
\ No newline at end of file

From 96b1d74fefd26ce5d2639eb6364cff11b21d7fa2 Mon Sep 17 00:00:00 2001
From: Michael Gecht <gecht.m@gmail.com>
Date: Fri, 19 Oct 2018 10:45:56 +0200
Subject: [PATCH 3/5] Add tests to migrations

---
 .../tests/migrations/test_mds_to_dtr.py       | 113 ++++++++++++++++++
 1 file changed, 113 insertions(+)
 create mode 100644 mdbenchmark/tests/migrations/test_mds_to_dtr.py

diff --git a/mdbenchmark/tests/migrations/test_mds_to_dtr.py b/mdbenchmark/tests/migrations/test_mds_to_dtr.py
new file mode 100644
index 00000000..50da0e4d
--- /dev/null
+++ b/mdbenchmark/tests/migrations/test_mds_to_dtr.py
@@ -0,0 +1,113 @@
+# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
+# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
+#
+# MDBenchmark
+# Copyright (c) 2017-2018 The MDBenchmark development team and contributors
+# (see the file AUTHORS for the full list of names)
+#
+# MDBenchmark is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# MDBenchmark is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with MDBenchmark.  If not, see <http://www.gnu.org/licenses/>.
+import os
+import uuid
+
+import datreant as dtr
+import pytest
+from mdbenchmark.migrations import mds_to_dtr
+
+
+def create_file(bundle, path, filename):
+    data = {
+        "mdsynthesis": {},
+        "categories": {
+            "name": "bench",
+            "started": "true",
+            "module": "gromacs/2016.3",
+            "host": "draco",
+            "time": 15,
+            "gpu": "false",
+            "nodes": 1,
+        },
+        "tags": [],
+    }
+
+    file = bundle.join(filename)
+    data = str(data).replace("'", '"')
+    file.write(str(data))
+
+    return str(file)
+
+
+@pytest.fixture
+def create_sim_files(tmpdir):
+    sim_files = []
+    directory = tmpdir.mkdir("draco_gromacs").mkdir("2018.1")
+    for path in ["1", "2", "3"]:
+        bundle = directory.mkdir(path)
+        filename = "Sim.{uid}.json".format(uid=uuid.uuid4())
+        sim = create_file(bundle, path, filename)
+        sim_files.append(sim)
+
+        proxy_filename = ".{filename}.proxy".format(filename=filename)
+        proxy = create_file(bundle, path, proxy_filename)
+        sim_files.append(proxy)
+
+        tpr = create_file(bundle, path, "md.tpr")
+        sim_files.append(tpr)
+
+    return directory, sim_files
+
+
+def test_search_mdsynthesis_sim_files(create_sim_files):
+    directory, files = create_sim_files
+
+    bundles = mds_to_dtr.search_mdsynthesis_sim_files(str(directory))
+    files = [file for file in files if file.endswith(".json")]
+    assert bundles == files
+
+
+def test_convert_to_datreant(create_sim_files):
+    directory, files = create_sim_files
+
+    sim_files = [file for file in files if file.endswith(".json")]
+    proxy_files = [file for file in files if file.endswith(".proxy")]
+    files_to_keep = [file for file in files if ".json" not in file]
+    mds_to_dtr.convert_to_datreant(sim_files)
+
+    for path in ["1", "2", "3"]:
+        # New directory and files exist
+        treant = os.path.join(str(directory), path, ".datreant")
+        assert os.path.exists(os.path.join(treant))
+        assert os.path.exists(os.path.join(treant, "categories.json"))
+
+    # Old files were deleted correctly, others were kept
+    for file in proxy_files:
+        assert not os.path.exists(file)
+    for file in files_to_keep:
+        assert os.path.exists(file)
+
+
+def test_migrate_to_datreant(tmpdir, capsys, create_sim_files):
+    directory, files = create_sim_files
+
+    with tmpdir.as_cwd():
+        assert mds_to_dtr.migrate_to_datreant(".") is None
+
+    mds_to_dtr.migrate_to_datreant(str(directory))
+    out, err = capsys.readouterr()
+
+    output = (
+        "Converting old benchmark metadata to new format!\n"
+        "Finished converting old benchmarks to new format!\n"
+    )
+
+    assert out == output

From 24325c0507ab66b740e964a74fdf0515da3b05d3 Mon Sep 17 00:00:00 2001
From: Michael Gecht <gecht.m@gmail.com>
Date: Fri, 19 Oct 2018 10:54:43 +0200
Subject: [PATCH 4/5] Add changelog fragment

---
 changelog/110.misc | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 changelog/110.misc

diff --git a/changelog/110.misc b/changelog/110.misc
new file mode 100644
index 00000000..7c1647e7
--- /dev/null
+++ b/changelog/110.misc
@@ -0,0 +1 @@
+Replaced ``mdsynthesis`` with ``datreant`` and upgraded to the new ``datreant>=1.0`` format.
\ No newline at end of file

From 2893c922409f5ebbad872e19702b60b43d3f67be Mon Sep 17 00:00:00 2001
From: Michael Gecht <gecht.m@gmail.com>
Date: Fri, 19 Oct 2018 12:42:17 +0200
Subject: [PATCH 5/5] Remove `mdbenchmark` package from pip install

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 8d2a9504..ab118afa 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -74,7 +74,7 @@ jobs:
 
 install:
   - $UPGRADE_PIP
-  - pip install . mdbenchmark -v $PYTEST_COV
+  - pip install . -v $PYTEST_COV
 
 script:
   - pytest $CODECOV