debian/TODO

-Replace
-
-    Testsuite: autopkgtest-pkg-python
-
-by a real test suite running build time tests

debian/changelog

@@ -2,12 +2,13 @@ python-treetime (0.5.0-1) unstable; urgency=medium
 
   * New upstream version
   * Drop ancient X-Python-Version field
-  * Provide Python3 package, move tools also to Python3 package
+  * Switch to Python3
   * Standards-Version: 4.2.1
-  * Build-Depends: python*-biopython, python*-numpy, python*-pandas,
-    python*-scipy
+  * Build-Depends: python3-biopython, python3-numpy, python3-pandas,
+    python3-scipy
+  * Recommends: python3-matplotlib
 
- -- Andreas Tille <tille@debian.org>  Thu, 27 Sep 2018 11:57:12 +0200
+ -- Andreas Tille <tille@debian.org>  Thu, 27 Sep 2018 14:45:27 +0200
 
 python-treetime (0.2.4-1) unstable; urgency=medium
 

debian/control

@@ -6,12 +6,6 @@ Testsuite: autopkgtest-pkg-python
 Priority: optional
 Build-Depends: debhelper (>= 11~),
                dh-python,
-               python-all,
-               python-biopython,
-               python-numpy,
-               python-pandas,
-               python-scipy,
-               python-setuptools,
                python3-all,
                python3-biopython,
                python3-numpy,
@@ -23,46 +17,6 @@ Vcs-Browser: https://salsa.debian.org/med-team/python-treetime
 Vcs-Git: https://salsa.debian.org/med-team/python-treetime.git
 Homepage: https://github.com/neherlab/treetime
 
-Package: python-treetime
-Architecture: all
-Section: python
-Depends: ${python:Depends},
-         ${misc:Depends},
-         python-numpy,
-         python-scipy,
-         python-biopython,
-         python-pandas
-Description: inference of time stamped phylogenies and ancestral reconstruction (Python 2)
- TreeTime provides routines for ancestral sequence reconstruction and the
- maximum likelihoo inference of molecular-clock phylogenies, i.e., a tree
- where all branches are scaled such that the locations of terminal nodes
- correspond to their sampling times and internal nodes are placed at the
- most likely time of divergence.
- .
- TreeTime aims at striking a compromise between sophisticated
- probabilistic models of evolution and fast heuristics. It implements GTR
- models of ancestral inference and branch length optimization, but takes
- the tree topology as given. To optimize the likelihood of time-scaled
- phylogenies, treetime uses an iterative approach that first infers
- ancestral sequences given the branch length of the tree, then optimizes
- the positions of unconstraine d nodes on the time axis, and then repeats
- this cycle. The only topology optimization are (optional) resolution of
- polytomies in a way that is most (approximately) consistent with the
- sampling time constraints on the tree. The package is designed to be
- used as a stand-alone tool or as a library used in larger phylogenetic
- analysis workflows.
- .
- Features
-  * ancestral sequence reconstruction (marginal and joint maximum
-    likelihood)
-  * molecular clock tree inference (marginal and joint maximum
-    likelihood)
-  * inference of GTR models
-  * rerooting to obtain best root-to-tip regression
-  * auto-correlated relaxed molecular clock (with normal prior)
- .
- This package provides the Python 2 module.
-
 Package: python3-treetime
 Architecture: all
 Section: python
@@ -72,6 +26,7 @@ Depends: ${python3:Depends},
          python3-scipy,
          python3-biopython,
          python3-pandas
+Recommends: python3-matplotlib
 Description: inference of time stamped phylogenies and ancestral reconstruction (Python 3)
  TreeTime provides routines for ancestral sequence reconstruction and the
  maximum likelihoo inference of molecular-clock phylogenies, i.e., a tree
@@ -102,41 +57,3 @@ Description: inference of time stamped phylogenies and ancestral reconstruction
   * auto-correlated relaxed molecular clock (with normal prior)
  .
  This package provides the Python 3 module.
-
-Package: python-treetime-examples
-Architecture: all
-Section: python
-Depends: ${python:Depends},
-         ${misc:Depends},
-         python-treetime
-Description: inference of time stamped phylogenies and ancestral reconstruction (example)
- TreeTime provides routines for ancestral sequence reconstruction and the
- maximum likelihoo inference of molecular-clock phylogenies, i.e., a tree
- where all branches are scaled such that the locations of terminal nodes
- correspond to their sampling times and internal nodes are placed at the
- most likely time of divergence.
- .
- TreeTime aims at striking a compromise between sophisticated
- probabilistic models of evolution and fast heuristics. It implements GTR
- models of ancestral inference and branch length optimization, but takes
- the tree topology as given. To optimize the likelihood of time-scaled
- phylogenies, treetime uses an iterative approach that first infers
- ancestral sequences given the branch length of the tree, then optimizes
- the positions of unconstraine d nodes on the time axis, and then repeats
- this cycle. The only topology optimization are (optional) resolution of
- polytomies in a way that is most (approximately) consistent with the
- sampling time constraints on the tree. The package is designed to be
- used as a stand-alone tool or as a library used in larger phylogenetic
- analysis workflows.
- .
- Features
-  * ancestral sequence reconstruction (marginal and joint maximum
-    likelihood)
-  * molecular clock tree inference (marginal and joint maximum
-    likelihood)
-  * inference of GTR models
-  * rerooting to obtain best root-to-tip regression
-  * auto-correlated relaxed molecular clock (with normal prior)
- .
- This package contains example scripts and data to test the usage of
- treetime.

debian/createmanpages

 #!/bin/sh
-MANDIR=debian/mans
+MANDIR=debian
 mkdir -p $MANDIR
 
 VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
@@ -8,23 +8,13 @@ AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian dist
 can be used for any other usage of the program.
 "
 
-progname=ancestral_reconstruction
+progname=treetime
 help2man --no-info --no-discard-stderr  \
-         --name='Reconstructs ancestral sequences and maps mutations to the tree' \
+         --name='Maximum Likelihood Phylodynamics' \
             --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
 echo $AUTHOR >> $MANDIR/${progname}.1
 
-progname=temporal_signal
-help2man --no-info --no-discard-stderr  \
-         --name="Calculates the root-to-tip regression and quantifies the 'clock-i-ness' of a tree" \
-            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
-echo $AUTHOR >> $MANDIR/${progname}.1
-
-progname=timetree_inference
-help2man --no-info --no-discard-stderr \
-         --name='Reconstructs ancestral sequences and infers a molecular clock tree' \
-            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
-echo $AUTHOR >> $MANDIR/${progname}.1
+echo "$MANDIR/*.1" > debian/manpages
 
 cat <<EOT
 Please enhance the help2man output.

debian/manpages

+debian/*.1

debian/mans/ancestral_reconstruction.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
-.TH ANCESTRAL_RECONSTRUCTION "1" "June 2017" "ancestral_reconstruction 0.0+20170607" "User Commands"
-.SH NAME
-ancestral_reconstruction \- Reconstructs ancestral sequences and maps mutations to the tree
-.SH SYNOPSIS
-.B ancestral_reconstruction
-[\-h] \fB\-\-aln\fR ALN \fB\-\-tree\fR TREE [\-\-prot] [\-\-marginal] [\-\-infer_gtr] [\-\-keep_overhangs]
-.PP
-.SH DESCRIPTION
-Reconstructs ancestral sequences and maps mutations to the tree. The output
-consists of a file ending with _ancestral.fasta with ancestral sequences and a
-tree ending with _mutation.nexus with mutations added as comments like
-_A45G_... The inferred GTR model is written to stdout
-.SH OPTIONS
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-show this help message and exit
-.TP
-\fB\-\-aln\fR ALN
-fasta file with input sequences
-.TP
-\fB\-\-tree\fR TREE
-newick file with tree
-.TP
-\fB\-\-prot\fR
-protein alignment
-.TP
-\fB\-\-marginal\fR
-marginal instead of joint ML reconstruction
-.TP
-\fB\-\-infer_gtr\fR
-infer substitution model
-.TP
-\fB\-\-keep_overhangs\fR
-do not fill terminal gaps
-.SH AUTHOR
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/temporal_signal.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
-.TH TEMPORAL_SIGNAL "1" "June 2017" "temporal_signal 0.0+20170607" "User Commands"
-.SH NAME
-temporal_signal \- Calculates the root-to-tip regression and quantifies the 'clock-i-ness' of a tree
-.SH SYNOPSIS
-.B temporal_signal
-[\-h] \fB\-\-tree\fR TREE \fB\-\-dates\fR DATES [\-\-aln ALN] [\-\-infer_gtr] [\-\-reroot] [\-\-plot] [\-\-verbose VERBOSE]
-.PP
-.SH DESCRIPTION
-Calculates the root\-to\-tip regression and quantifies the 'clock\-i\-ness' of the
-tree. It will optionally reroot the tree to maximize the clock\-like signal and
-recalculate branch length.
-.SH OPTIONS
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-show this help message and exit
-.TP
-\fB\-\-tree\fR TREE
-newick file with tree
-.TP
-\fB\-\-dates\fR DATES
-csv with dates for nodes with 'node_name, date' where
-date is float (as in 2012.15)
-.TP
-\fB\-\-aln\fR ALN
-fasta file with input sequences
-.TP
-\fB\-\-infer_gtr\fR
-infer substitution model
-.TP
-\fB\-\-reroot\fR
-reroot the tree to maximize the correlation of root\-totip distance with sampling time
-.HP
-\fB\-\-plot\fR
-.TP
-\fB\-\-verbose\fR VERBOSE
-verbosity of output 0\-6
-.SH AUTHOR
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/mans/timetree_inference.1

-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
-.TH TIMETREE_INFERENCE "1" "June 2017" "timetree_inference 0.0+20170607" "User Commands"
-.SH NAME
-timetree_inference \- Reconstructs ancestral sequences and infers a molecular clock tree
-.SH SYNOPSIS
-.B timetree_inference
-[\-h] \fB\-\-aln\fR ALN \fB\-\-tree\fR TREE \fB\-\-dates\fR DATES
-[\-\-infer_gtr] [\-\-reroot REROOT]
-[\-\-resolve_polytomies] [\-\-relax [RELAX [RELAX ...]]]
-[\-\-max_iter MAX_ITER] [\-\-verbose VERBOSE] [\-\-Tc TC]
-[\-\-plot]
-.PP
-.SH DESCRIPTION
-Reconstructs ancestral sequences and infers a molecular clock tree. The output
-consists of a file ending with _ancestral.fasta with ancestral sequences and a
-tree ending with _mutation.newick with mutations appended to node names as
-_A45G_.... The branches of this tree are scaled such that branch length
-correspond to times in units of the molecular clock. The molecular clock,
-along with the inferred GTR model, is written to stdout
-.SH OPTIONS
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-show this help message and exit
-.TP
-\fB\-\-aln\fR ALN
-fasta file with input sequences
-.TP
-\fB\-\-tree\fR TREE
-newick file with tree
-.TP
-\fB\-\-dates\fR DATES
-csv with dates for nodes with 'node_name, date' where
-date is float (as in 2012.15)
-.TP
-\fB\-\-infer_gtr\fR
-infer substitution model
-.TP
-\fB\-\-reroot\fR REROOT
-reroot the tree. Valid arguments are 'best',
-\&'midpoint', or a node name
-.TP
-\fB\-\-resolve_polytomies\fR
-resolve polytomies using temporal information.
-.TP
-\fB\-\-relax\fR [RELAX [RELAX ...]]
-use an autocorrelated molecular clock. Prior strength
-and coupling of parent and offspring rates can be
-specified e.g. as \fB\-\-relax\fR 1.0 0.5
-.TP
-\fB\-\-max_iter\fR MAX_ITER
-maximal number of iterations the inference cycle is
-run
-.TP
-\fB\-\-verbose\fR VERBOSE
-verbosity of output 0\-6
-.TP
-\fB\-\-Tc\fR TC
-coalescent time scale \fB\-\-\fR sensible values are on the
-order of the average hamming distance of
-contemporaneous sequences
-.TP
-\fB\-\-plot\fR
-plot the tree on a time axis
-.SH AUTHOR
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

debian/python-treetime-examples.install

-# data	usr/share/doc/python-treetime
-test	usr/share/doc/python-treetime

debian/python3-treetime.examples

+test

debian/python3-treetime.install

-*.py	usr/share/treetime

debian/python3-treetime.manpages

-debian/mans/*.1

debian/rules

@@ -7,14 +7,9 @@ export PYBUILD_NAME = treetime
 EXECDIR=debian/python3-$(PYBUILD_NAME)/usr/share/treetime
 
 %:
-	dh $@ --with python2,python3 --buildsystem=pybuild
+	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_install:
 	dh_install
-	find debian/*/usr/share/treetime -name __init__.py -delete
-	find debian/*/usr/share/treetime -name setup.py -delete
 	## enable dh_python finding dependency
-	find debian/*/usr/lib/*/dist-packages/treetime -name "*.py" -exec sed -i 's:/usr/local/bin/python:/usr/bin/python:' \{\} \;
-	mkdir -p $(EXECDIR)
-	mv debian/python-$(PYBUILD_NAME)/usr/bin/* $(EXECDIR)
-	dh_link -p python3-$(PYBUILD_NAME)	usr/share/$(PYBUILD_NAME)/$(PYBUILD_NAME)	usr/bin/$(PYBUILD_NAME)
+	find debian -name "*.py" -exec sed -i '1s:/usr/local/bin/python:/usr/bin/python:' \{\} \;

debian/treetime.1

+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
+.TH TREETIME "1" "September 2018" "treetime 0.5.0" "User Commands"
+.SH NAME
+treetime \- Maximum Likelihood Phylodynamics
+.SH SYNOPSIS
+.B treetime
+<positional> [optional]
+.SH DESCRIPTION
+TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies, i.e., a tree where all branches are scaled such that the positions of terminal nodes correspond to their sampling times and internal nodes are placed at the most likely time of divergence.
+.P
+To optimize the likelihood of time-scaled phylogenies, TreeTime uses an iterative approach that first infers ancestral sequences given the branch length of the tree, then optimizes the positions of unconstrained nodes on the time axis, and then repeats this cycle. The only topology optimization are (optional) resolution of polytomies in a way that is most (approximately) consistent with the sampling time constraints on the tree. The package is designed to be used as a stand-alone tool on the command-line or as a library used in larger phylogenetic analysis work-flows.
+.SH OPTIONS
+.SS positional arguments
+.TP
+\fBancestral\fR
+infer ancestral sequences maximizing the joint or marginal likelihood.
+.TP
+\fBhomoplasy\fR
+analyze patterns of recurrent mutations aka homoplasies.
+.TP
+\fBclock\fR
+estimate molecular clock parameters and reroot the tree.
+.TP
+\fBmugration\fR
+map discrete character such as host or country to the tree.
+.SS optional arguments
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-tree\fR TREE
+Name of file containing the tree in newick, nexus, or
+phylip format. If none is provided, treetime will
+attempt to build a tree from the alignment using
+fasttree, iqtree, or raxml (assuming they are
+installed)
+.TP
+\fB\-\-sequence\-length\fR SEQUENCE_LENGTH
+length of the sequence, used to calculate expected
+variation in branch length. Not required if alignment
+is provided.
+.TP
+\fB\-\-aln\fR ALN
+alignment file (fasta)
+.TP
+\fB\-\-vcf\-reference\fR VCF_REFERENCE
+only for vcf input: fasta file of the sequence the VCF
+was mapped to.
+.TP
+\fB\-\-dates\fR DATES
+csv file with dates for nodes with 'node_name, date'
+where date is float (as in 2012.15)
+.TP
+\fB\-\-clock\-filter\fR CLOCK_FILTER
+ignore tips that don't follow a loose clock, 'clockfilter=number of interquartile ranges from regression'
+.TP
+\fB\-\-reroot\fR REROOT
+reroot the tree. Valid choices are 'ML', 'ML\-rough',
+\&'least\-squares', 'min_dev', 'midpoint' or a node name
+to be used as outgroup. Use \fB\-\-keep\-root\fR to keep the
+current root.
+.TP
+\fB\-\-keep\-root\fR
+don't reroot the tree. Otherwise, reroot to minimize
+the the residual of the regression of root\-to\-tip
+distance and sampling time
+.TP
+\fB\-\-gtr\fR GTR
+GTR model to use. '\-\-gtr infer' will infer a model
+from the data. Alternatively, specify the model type.
+If the specified model requires additional options,
+use '\-\-gtr\-params' to specify those.
+.TP
+\fB\-\-gtr\-params\fR GTR_PARAMS [GTR_PARAMS ...]
+GTR parameters for the model specified by the \fB\-\-gtr\fR
+argument. The parameters should be feed as 'key=value'
+list of parameters. Example: '\-\-gtr K80 \fB\-\-gtr\-params\fR
+kappa=0.2 pis=0.25,0.25,0.25,0.25'. See the exact
+definitions of the parameters in the GTR creation
+methods in treetime/nuc_models.py or
+treetime/aa_models.py
+.TP
+\fB\-\-clock\-rate\fR CLOCK_RATE
+if specified, the rate of the molecular clock won't be
+optimized.
+.TP
+\fB\-\-branch\-length\-mode\fR {auto,input,joint,marginal}
+If set to 'input', the provided branch length will be
+used without modification. Note that branch lengths
+optimized by treetime are only accurate at short
+evolutionary distances.
+.TP
+\fB\-\-confidence\fR
+estimate confidence intervals of divergence times.
+.TP
+\fB\-\-keep\-polytomies\fR
+Don't resolve polytomies using temporal information.
+.TP
+\fB\-\-relax\fR [RELAX [RELAX ...]]
+use an autocorrelated molecular clock. Prior strength
+and coupling of parent and offspring rates can be
+specified e.g. as \fB\-\-relax\fR 1.0 0.5
+.TP
+\fB\-\-max\-iter\fR MAX_ITER
+maximal number of iterations the inference cycle is
+run. Note that for polytomy resolution and coalescence
+models max_iter should be at least 2
+.TP
+\fB\-\-coalescent\fR COALESCENT
+coalescent time scale \fB\-\-\fR sensible values are on the
+order of the average hamming distance of
+contemporaneous sequences. In addition, 'opt'
+\&'skyline' are valid options and estimate a constant
+coalescent rate or a piecewise linear coalescent rate
+history
+.TP
+\fB\-\-plot\-tree\fR PLOT_TREE
+filename to save the plot to. Suffix will determine
+format (choices pdf, png, svg, default=pdf)
+.TP
+\fB\-\-plot\-rtt\fR PLOT_RTT
+filename to save the plot to. Suffix will determine
+format (choices pdf, png, svg, default=pdf)
+.TP
+\fB\-\-keep\-overhangs\fR
+do not fill terminal gaps
+.TP
+\fB\-\-zero\-based\fR
+zero based mutation indexing
+.TP
+\fB\-\-report\-ambiguous\fR
+include transitions involving ambiguous states
+.TP
+\fB\-\-verbose\fR VERBOSE
+verbosity of output 0\-6
+.TP
+\fB\-\-outdir\fR OUTDIR
+directory to write the output to
+.SH SEE ALSO
+https://github.com/neherlab/treetime
+.SH EXAMPLES
+https://github.com/neherlab/treetime_examples
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.