fasttree building

CHANGELOG.rst

@@ -3,6 +3,15 @@ Changelog
 
 .. snip
 
+
+
+- Setuptools >30 is now required, due to moving many things into setup.cfg.
+
+- FastTree source now included in distribution; FastTree binary will be built
+  and put in virtual environment under name ``FastTree-lorax``.
+
+- License is now 3-clause BSD (was 4-clause BSD).
+
 -  ``config_value`` command is now simply ``config``.
 
 0.93.2

INSTALL.anaconda.txt

@@ -0,0 +1,27 @@
+lorax was tested under Anaconda Python 3.6.  
+
+lorax requires some packages that are in the bioconda channel, so before
+installing lorax, the following channels must be added:
+
+	conda config --add channels conda-forge
+	conda config --add channels defaults
+	conda config --add channels r
+	conda config --add channels bioconda
+
+After the channels are configured, the following dependencies should be
+added.  I prefer adding them to the root installation, but you may prefer
+to add them to the virtual environment to be constructed later:
+
+	conda install biopython redis redis-py hmmer gcc libgcc raxml
+
+Next, it is highly recommended that you create a virtual environment for
+lorax to run in.  lorax depends on a version of setuptools that is
+currently much higher than the version required by anaconda, so you may
+break other packages if you install lorax in a shared environment:
+
+	conda create --name loraxenv biopython click croniter flask \
+	  gcc libgcc raxml redis redis-py itsdangerous jinja2 markupsafe \
+	  python-dateutil rq six werkzeug
+
+After installing these packages then, "pip install lorax" should get the
+remaining packages directly from pypi.

LICENSE.txt

@@ -3,25 +3,26 @@ Copyright (c) 2017, The National Center for Genome Resources
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
-1. Redistributions of source code must retain the above copyright
-   notice, this list of conditions and the following disclaimer.
-2. Redistributions in binary form must reproduce the above copyright
-   notice, this list of conditions and the following disclaimer in the
-   documentation and/or other materials provided with the distribution.
-3. All advertising materials mentioning features or use of this software
-   must display the following acknowledgement:
-   This product includes software developed by The National Center for Genome Resources.
-4. Neither the name of NCGR nor the names of its contributors may be used
-   to endorse or promote products derived from this software without specific
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of NCGR nor the names of its contributors may be used to
+   endorse or promote products derived from this software without specific
    prior written permission.
 
-This software is provided by NCGR "as is" and any express or implied
-warranties, including, but not limited to, the implied warranties of
-merchantability and fitness for a particular purpose are disclaimed.
-In no event shall NCGR be liable for any direct, indirect, incidental,
-special, exemplary, or consequential damages (including, but not limited
-to, procurement of substitute goods or services; loss of use, data, or
-profits; or business interruption) however caused and on any theory of
-liability, whether in contract, strict liability, or tort (including
-negligence or otherwise) arising in any way out of the use of this software,
-even if advised of the possibility of such damage.
+THIS SOFTWARE IS PROVIDED BY NCGR AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR
+IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO
+EVENT SHALL NCGR OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
+OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+

MANIFEST.in

@@ -1,7 +1,8 @@
 include *.txt
 include INSTALL.*
-recursive-include lorax/instance *
 recursive-include lorax/test *
 recursive-include lorax/static *
 recursive-include lorax/templates *
 recursive-include lorax/fasttree *
+prune lorax/test/data
+prune lorax/test/logs

lorax/__init__.py

@@ -15,6 +15,7 @@
 import io
 import json
 import os
+import platform
 import shutil
 import subprocess
 from collections import OrderedDict  # python 3.1
@@ -219,19 +220,25 @@ def run_subprocess_with_status(out_path,
     :param status_path: Path to status log file
     :return: Return code of subprocess
     """
+    environ = os.environ.copy()
     #
     # Modify the environment to select the number of threads, if requested.
     #
-    environ = os.environ.copy()
     if app.config['THREADS'] > 0:
         environ['OMP_NUM_THREADS'] = str(app.config['THREADS'])
-    with out_path.open(mode='wb') as out_fh:
-        with err_path.open(mode='wt') as err_fh:
-            status = subprocess.run(cmdlist,
-                                    stdout=out_fh,
-                                    stderr=err_fh,
-                                    cwd=str(cwd),
-                                    env=environ)
+    #
+    # Export DYLD_LIBRARY_PATH so that FastTree-lorax will run
+    # on MacOSX.
+    #
+    #if platform.system == 'Darwin':
+    #    environ['DYLDLIBRARY_PATH']  = str(Path(sys.prefix).resolve() /'lib')
+    #with out_path.open(mode='wb') as out_fh:
+    #    with err_path.open(mode='wt') as err_fh:
+    #        status = subprocess.run(cmdlist,
+    #                                stdout=out_fh,
+    #                                stderr=err_fh,
+    #                                cwd=str(cwd),
+    #                                env=environ)
     write_status(status_path, status.returncode)
     if post_process is not None:
         post_process(out_path,

lorax/cli.py

@@ -227,6 +227,17 @@ def config(var, value, vartype, verbose):
                   file=config_fh)  # noqa
 
 
+
+@cli.command()
+def delete_config():
+    """Deletes the config file."""
+    config_file_path = Path(current_app.instance_path) / current_app.config[
+        'SETTINGS']
+    if config_file_path.exists():
+        print('Deleting config file %s.' %(str(config_file_path)))
+        config_file_path.unlink()
+
+
 @cli.command()
 def test_logging():
     """Test logging at the different levels.

lorax/config.py

@@ -104,7 +104,7 @@ class BaseConfig(object):
             "DNA": ["-d"]
         }
     }
-    FASTTREE_EXE = 'FastTree'
+    FASTTREE_EXE = 'FastTree-lorax'
     RAXML_EXE = 'raxmlHPC'
     #
     # Logging formatter.  Fields that are defined are:

lorax/version.py

@@ -1,2 +1,2 @@
 # coding: utf-8
-version = '0.93.3'
+version = '0.93.5'

requirements.in

@@ -1,5 +1,6 @@
 # requirements.in
-Flask_RQ2
+packaging
+setuptools>30.3.0
+Flask_RQ2[cli]
 biopython
 rq-dashboard
-gunicorn

requirements.txt

@@ -4,20 +4,22 @@
 #
 #    pip-compile --output-file requirements.txt requirements.in
 #
+appdirs==1.4.3            # via setuptools
 arrow==0.10.0             # via rq-dashboard
-biopython==1.68
-click==6.7                # via flask, rq
-croniter==0.3.16          # via rq-scheduler
-flask-rq2==17.0
-flask==0.12.1             # via flask-rq2, rq-dashboard
-gunicorn==19.7.1
+biopython==1.69
+click==6.7                # via flask, flask-cli, rq
+croniter==0.3.17          # via rq-scheduler
+flask-cli==0.4.0          # via flask-rq2
+flask-rq2[cli]==17.0
+flask==0.12.2             # via flask-cli, flask-rq2, rq-dashboard
 itsdangerous==0.24        # via flask
 jinja2==2.9.6             # via flask
-markupsafe==0.23          # via jinja2 --edited for version
+markupsafe==1.0           # via jinja2
+packaging==16.8
 python-dateutil==2.6.0    # via arrow, croniter
-redis                     # via rq, rq-dashboard --edited to allow 3.2.0
+redis==2.10.5             # via rq, rq-dashboard
 rq-dashboard==0.3.7
 rq-scheduler==0.7.0       # via flask-rq2
 rq==0.6.0                 # via flask-rq2, rq-dashboard, rq-scheduler
-six==1.10.0               # via python-dateutil
-werkzeug==0.12.1          # via flask
+six==1.10.0               # via python-dateutil, setuptools
+werkzeug==0.12.2          # via flask

setup.cfg

@@ -1,8 +1,73 @@
 [metadata]
-description-file = README.rst
+name = lorax
+provides = lorax
+version = attr:lorax.version.version
+url = http://github.com/ncgr/lorax
+description = Server for phylogenetic tree generation and extension
+author = Joel Berendzen
+author_email = [email protected]
+maintainer = Joel Berendzen
+maintainer_email = [email protected]
+long_description = file:README.rst
+description-file =
+    README.rst
+    CHANGELOG.rst
+keywords =
+    science
+    biology
+    bioinformatics
+    genomics
+    phylogeny
+    genes
+    gene families
+    multiple sequence alignment
+    phylogenetic trees
+license = BSD 3-Clause License
+license_file = LICENSE.txt
+platforms = any
+classifiers =
+    Development Status :: 4 - Beta,
+    Environment :: Console,
+    Framework :: Flask,
+    Intended Audience :: Science/Research,
+    License :: OSI Approved :: BSD License,
+    Operating System :: OS Independent,
+    Programming Language :: Python :: 3.4,
+    Programming Language :: Python :: 3.5,
+    Programming Language :: Python :: 3.6,
+    Topic :: Scientific/Engineering :: Bio-Informatics
 
-[bdist-wheel]
+[options]
+zip_safe = False
+include_package_data = True
+packages = lorax
+install_requires =
+    Flask-RQ2[cli]
+    biopython
+    rq_dashboard
+
+[options.package_data]
+* =
+    *.txt
+    *.rst
+    *.html
+    *.c
+    *.faa
+    *.hmm
+    *.sh
+    *.css
+    *.js
+    favicon.ico
+
+[options.packages.find]
+exclude =
+    lorax.test.data
+    lorax.test.logs
+
+[bdist_wheel]
 universal = 0
 
 [wheel]
 universal = 0
+
+