[med-svn] [Git][med-team/phyx][master] 5 commits: whatis.patch: new: give meaningful manual pages descriptions.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Tue Aug 15 09:46:58 BST 2023
Étienne Mollier pushed to branch master at Debian Med / phyx
Commits:
4c3d7d91 by Étienne Mollier at 2023-08-15T10:34:46+02:00
whatis.patch: new: give meaningful manual pages descriptions.
- - - - -
a810af4e by Étienne Mollier at 2023-08-15T10:35:17+02:00
hardening.patch: new: propagate hardening flags.
- - - - -
9a4df168 by Étienne Mollier at 2023-08-15T10:41:11+02:00
d/lintian-overrides: hide hardening no fortifiable information.
Some programs part of the phyx distribution do not seem fortifiable at
all in spite of the propagation of the appropriate preprocessor flags.
- - - - -
4cb7a4d7 by Étienne Mollier at 2023-08-15T10:45:05+02:00
hardening.patch: dep3 header
Gbp-Dch: ignore
- - - - -
3fce76be by Étienne Mollier at 2023-08-15T10:46:09+02:00
ready to upload to unstable.
- - - - -
5 changed files:
- debian/changelog
- + debian/lintian-overrides
- + debian/patches/hardening.patch
- debian/patches/series
- + debian/patches/whatis.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,15 @@
-phyx (1.3.1+ds-2) UNRELEASED; urgency=medium
+phyx (1.3.1+ds-2) unstable; urgency=medium
* d/rules: build with -ffunction-sections on hppa.
Thanks to John David Anglin (Closes: #1044139)
* d/control: add myself to uploaders.
+ * whatis.patch: new: give meaningful manual pages descriptions.
+ * hardening.patch: new: propagate hardening flags.
+ * d/lintian-overrides: hide hardening no fortifiable information.
+ Some programs part of the phyx distribution do not seem fortifiable at
+ all in spite of the propagation of the appropriate preprocessor flags.
- -- Étienne Mollier <emollier at debian.org> Mon, 14 Aug 2023 17:28:49 +0200
+ -- Étienne Mollier <emollier at debian.org> Tue, 15 Aug 2023 10:45:37 +0200
phyx (1.3.1+ds-1) unstable; urgency=medium
=====================================
debian/lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+# A bunch of programs do not seem fortifiable even though the appropriate build
+# flags are passed, so let's put them off the radar for now.
+phyx: hardening-no-fortify-functions [usr/bin/px*]
=====================================
debian/patches/hardening.patch
=====================================
@@ -0,0 +1,293 @@
+Description: propagate preprocessor and linker flags.
+ This allows the programs to benefit from flags for implementing hardening.
+ For some reason, a bunch of programs are still flagged as missing the
+ appropriate preprocessor flags, although they are indeed passed per build log.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2023-08-15
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- phyx.orig/src/Makefile.in
++++ phyx/src/Makefile.in
+@@ -373,102 +373,102 @@
+
+ pxlssq: $(CPP_OBJS) $(SEQ_OBJS) $(LS_SQ_OBJ)
+ @echo 'bulding pxlssq'
+- $(CXX) $(CXXFLAGS) -o "pxlssq" $(OPT_FLAGS) $(LS_SQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxlssq" $(OPT_FLAGS) $(LS_SQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxconsq: $(CPP_OBJS) $(SEQ_OBJS) $(CONSEQ_OBJ)
+ @echo 'building pxconsq'
+- $(CXX) $(CXXFLAGS) -o "pxconsq" $(OPT_FLAGS) $(CONSEQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxconsq" $(OPT_FLAGS) $(CONSEQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxclsq: $(CPP_OBJS) $(SEQ_OBJS) $(CLSQ_OBJ)
+ @echo 'building pxclsq'
+- $(CXX) $(CXXFLAGS) -o "pxclsq" $(OPT_FLAGS) $(CLSQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxclsq" $(OPT_FLAGS) $(CLSQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxrms: $(CPP_OBJS) $(SEQ_OBJS) $(RMS_OBJ)
+ @echo 'building pxrms'
+- $(CXX) $(CXXFLAGS) -o "pxrms" $(OPT_FLAGS) $(RMS_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxrms" $(OPT_FLAGS) $(RMS_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxaa2cdn: $(CPP_OBJS) $(SEQ_OBJS) $(AA2C_OBJ)
+ @echo 'building pxaa2cdn'
+- $(CXX) $(CXXFLAGS) -o "pxaa2cdn" $(OPT_FLAGS) $(AA2C_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxaa2cdn" $(OPT_FLAGS) $(AA2C_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxs2fa: $(CPP_OBJS) $(SEQ_OBJS) $(2FA_OBJ)
+ @echo 'building pxs2fa'
+- $(CXX) $(CXXFLAGS) -o "pxs2fa" $(OPT_FLAGS) $(2FA_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxs2fa" $(OPT_FLAGS) $(2FA_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxs2phy: $(CPP_OBJS) $(SEQ_OBJS) $(2PHY_OBJ)
+ @echo 'building pxs2phy'
+- $(CXX) $(CXXFLAGS) -o "pxs2phy" $(OPT_FLAGS) $(2PHY_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxs2phy" $(OPT_FLAGS) $(2PHY_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxs2nex: $(CPP_OBJS) $(SEQ_OBJS) $(2NEX_OBJ)
+ @echo 'building pxs2nex'
+- $(CXX) $(CXXFLAGS) -o "pxs2nex" $(OPT_FLAGS) $(2NEX_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxs2nex" $(OPT_FLAGS) $(2NEX_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxfqfilt: $(CPP_OBJS) $(SEQ_OBJS) $(FQFILT_OBJ)
+ @echo 'building pxfqfilt'
+- $(CXX) $(CXXFLAGS) -o "pxfqfilt" $(OPT_FLAGS) $(FQFILT_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxfqfilt" $(OPT_FLAGS) $(FQFILT_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxrevcomp: $(CPP_OBJS) $(SEQ_OBJS) $(REVCOMP_OBJ)
+ @echo 'building pxrevcomp'
+- $(CXX) $(CXXFLAGS) -o "pxrevcomp" $(OPT_FLAGS) $(REVCOMP_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxrevcomp" $(OPT_FLAGS) $(REVCOMP_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxnw: $(CPP_OBJS) $(SEQ_OBJS) $(NW_OBJ)
+ @echo 'building pxnw'
+- $(CXX) $(CXXFLAGS) -o "pxnw" $(OPT_FLAGS) $(NW_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxnw" $(OPT_FLAGS) $(NW_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxsw: $(CPP_OBJS) $(SEQ_OBJS) $(SW_OBJ)
+ @echo 'building pxsw'
+- $(CXX) $(CXXFLAGS) -o "pxsw" $(OPT_FLAGS) $(SW_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxsw" $(OPT_FLAGS) $(SW_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxboot: $(CPP_OBJS) $(SEQ_OBJS) $(SEQSAMP_OBJ)
+ @echo 'building pxboot'
+- $(CXX) $(CXXFLAGS) -o "pxboot" $(OPT_FLAGS) $(SEQSAMP_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxboot" $(OPT_FLAGS) $(SEQSAMP_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxtlate: $(CPP_OBJS) $(SEQ_OBJS) $(TLATE_OBJ)
+ @echo 'building pxtlate'
+- $(CXX) $(CXXFLAGS) -o "pxtlate" $(OPT_FLAGS) $(TLATE_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxtlate" $(OPT_FLAGS) $(TLATE_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxcat: $(CPP_OBJS) $(SEQ_OBJS) $(CONCAT_OBJ)
+ @echo 'building pxcat'
+- $(CXX) $(CXXFLAGS) -o "pxcat" $(OPT_FLAGS) $(CONCAT_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxcat" $(OPT_FLAGS) $(CONCAT_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxsstat: $(CPP_OBJS) $(SEQ_OBJS) $(SSTAT_OBJ)
+ @echo 'building pxsstat'
+- $(CXX) $(CXXFLAGS) -o "pxsstat" $(OPT_FLAGS) $(SSTAT_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxsstat" $(OPT_FLAGS) $(SSTAT_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxrecode: $(CPP_OBJS) $(SEQ_OBJS) $(SEQRECODE_OBJ)
+ @echo 'building pxrecode'
+- $(CXX) $(CXXFLAGS) -o "pxrecode" $(OPT_FLAGS) $(SEQRECODE_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxrecode" $(OPT_FLAGS) $(SEQRECODE_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxssort: $(CPP_OBJS) $(SEQ_OBJS) $(SSORT_OBJ)
+ @echo 'building pxssort'
+- $(CXX) $(CXXFLAGS) -o "pxssort" $(OPT_FLAGS) $(SSORT_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxssort" $(OPT_FLAGS) $(SSORT_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxcomp: $(CPP_OBJS) $(SEQ_OBJS) $(COMPTEST_OBJ)
+ @echo 'building pxcomp'
+- $(CXX) $(CXXFLAGS) -o "pxcomp" $(OPT_FLAGS) $(COMPTEST_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxcomp" $(OPT_FLAGS) $(COMPTEST_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxvcf2fa: $(CPP_OBJS) $(SEQ_OBJS) $(VCF2FA_OBJ)
+ @echo 'building pxvcf2fa'
+- $(CXX) $(CXXFLAGS) -o "pxvcf2fa" $(OPT_FLAGS) $(VCF2FA_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxvcf2fa" $(OPT_FLAGS) $(VCF2FA_OBJ) $(CPP_OBJS) $(SEQ_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxssplit: $(CPP_OBJS) $(SEQ_OBJS) $(SEQ_SPLIT_OBJ)
+@@ -481,7 +481,7 @@
+
+ pxbdsim: $(CPP_OBJS) $(TREE_OBJS) $(BD_SIM_OBJ)
+ @echo 'building pxbdsim'
+- $(CXX) $(CXXFLAGS) -o "pxbdsim" $(OPT_FLAGS) $(BD_SIM_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxbdsim" $(OPT_FLAGS) $(BD_SIM_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxbdfit: $(CPP_OBJS) $(TREE_OBJS) $(BD_FIT_OBJ)
+@@ -496,102 +496,102 @@
+
+ pxlstr: $(CPP_OBJS) $(TREE_OBJS) $(LS_TR_OBJ)
+ @echo 'building pxlstr'
+- $(CXX) $(CXXFLAGS) -o "pxlstr" $(OPT_FLAGS) $(LS_TR_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxlstr" $(OPT_FLAGS) $(LS_TR_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxmrca: $(CPP_OBJS) $(TREE_OBJS) $(MRCA_OBJ)
+ @echo 'building pxmrca'
+- $(CXX) $(CXXFLAGS) -o "pxmrca" $(OPT_FLAGS) $(MRCA_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxmrca" $(OPT_FLAGS) $(MRCA_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxmrcacut: $(CPP_OBJS) $(TREE_OBJS) $(MRCACUT_OBJ)
+ @echo 'building pxmrcacut'
+- $(CXX) $(CXXFLAGS) -o "pxmrcacut" $(OPT_FLAGS) $(MRCACUT_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxmrcacut" $(OPT_FLAGS) $(MRCACUT_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxmrcaname: $(CPP_OBJS) $(TREE_OBJS) $(MRCANAME_OBJ)
+ @echo 'building pxmrcaname'
+- $(CXX) $(CXXFLAGS) -o "pxmrcaname" $(OPT_FLAGS) $(MRCANAME_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxmrcaname" $(OPT_FLAGS) $(MRCANAME_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxcltr: $(CPP_OBJS) $(TREE_OBJS) $(CLTR_OBJ)
+ @echo 'building pxcltr'
+- $(CXX) $(CXXFLAGS) -o "pxcltr" $(OPT_FLAGS) $(CLTR_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxcltr" $(OPT_FLAGS) $(CLTR_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxt2new: $(CPP_OBJS) $(TREE_OBJS) $(T2NEW_OBJ)
+ @echo 'building pxt2new'
+- $(CXX) $(CXXFLAGS) -o "pxt2new" $(OPT_FLAGS) $(T2NEW_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxt2new" $(OPT_FLAGS) $(T2NEW_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxt2nex: $(CPP_OBJS) $(TREE_OBJS) $(T2NEX_OBJ)
+ @echo 'building pxt2nex'
+- $(CXX) $(CXXFLAGS) -o "pxt2nex" $(OPT_FLAGS) $(T2NEX_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxt2nex" $(OPT_FLAGS) $(T2NEX_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxrr: $(CPP_OBJS) $(TREE_OBJS) $(RR_OBJ)
+ @echo 'building pxrr'
+- $(CXX) $(CXXFLAGS) -o "pxrr" $(OPT_FLAGS) $(RR_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxrr" $(OPT_FLAGS) $(RR_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxmono: $(CPP_OBJS) $(TREE_OBJS) $(MONO_OBJ)
+ @echo 'building pxmono'
+- $(CXX) $(CXXFLAGS) -o "pxmono" $(OPT_FLAGS) $(MONO_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxmono" $(OPT_FLAGS) $(MONO_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxrmt: $(CPP_OBJS) $(TREE_OBJS) $(RMT_OBJ)
+ @echo 'building pxrmt'
+- $(CXX) $(CXXFLAGS) -o "pxrmt" $(OPT_FLAGS) $(RMT_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxrmt" $(OPT_FLAGS) $(RMT_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxtrt: $(CPP_OBJS) $(TREE_OBJS) $(TRT_OBJ)
+ @echo 'building pxtrt'
+- $(CXX) $(CXXFLAGS) -o "pxtrt" $(OPT_FLAGS) $(TRT_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxtrt" $(OPT_FLAGS) $(TRT_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxrmk: $(CPP_OBJS) $(TREE_OBJS) $(RMK_OBJ)
+ @echo 'building pxrmk'
+- $(CXX) $(CXXFLAGS) -o "pxrmk" $(OPT_FLAGS) $(RMK_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxrmk" $(OPT_FLAGS) $(RMK_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxlog: $(CPP_OBJS) $(TREE_OBJS) $(LOGMANIP_OBJ)
+ @echo 'building pxlog'
+- $(CXX) $(CXXFLAGS) -o "pxlog" $(OPT_FLAGS) $(LOGMANIP_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxlog" $(OPT_FLAGS) $(LOGMANIP_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxtscale: $(CPP_OBJS) $(TREE_OBJS) $(RESCALE_TREE_OBJ)
+ @echo 'building pxtscale'
+- $(CXX) $(CXXFLAGS) -o "pxtscale" $(OPT_FLAGS) $(RESCALE_TREE_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxtscale" $(OPT_FLAGS) $(RESCALE_TREE_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxtcol: $(CPP_OBJS) $(TREE_OBJS) $(TCOL_OBJ)
+ @echo 'building pxtcol'
+- $(CXX) $(CXXFLAGS) -o "pxtcol" $(OPT_FLAGS) $(TCOL_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxtcol" $(OPT_FLAGS) $(TCOL_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxtcomb: $(CPP_OBJS) $(TREE_OBJS) $(TCOMB_OBJ)
+ @echo 'building pxtcomb'
+- $(CXX) $(CXXFLAGS) -o "pxtcomb" $(OPT_FLAGS) $(TCOMB_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxtcomb" $(OPT_FLAGS) $(TCOMB_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxtgen: $(CPP_OBJS) $(TREE_OBJS) $(TGEN_OBJ)
+ @echo 'building pxtgen'
+- $(CXX) $(CXXFLAGS) -o "pxtgen" $(OPT_FLAGS) $(TGEN_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxtgen" $(OPT_FLAGS) $(TGEN_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxpoly: $(CPP_OBJS) $(TREE_OBJS) $(POLY_OBJ)
+ @echo 'building pxpoly'
+- $(CXX) $(CXXFLAGS) -o "pxpoly" $(OPT_FLAGS) $(POLY_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxpoly" $(OPT_FLAGS) $(POLY_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxcolt: $(CPP_OBJS) $(TREE_OBJS) $(COLLAPSE_TREE_OBJ)
+ @echo 'building pxcolt'
+- $(CXX) $(CXXFLAGS) -o "pxcolt" $(OPT_FLAGS) $(COLLAPSE_TREE_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxcolt" $(OPT_FLAGS) $(COLLAPSE_TREE_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxbp: $(CPP_OBJS) $(TREE_OBJS) $(BP_OBJ)
+ @echo 'building pxbp'
+- $(CXX) $(CXXFLAGS) -o "pxbp" $(OPT_FLAGS) $(BP_OBJ) $(CPP_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxbp" $(OPT_FLAGS) $(BP_OBJ) $(CPP_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+
+@@ -599,22 +599,22 @@
+
+ pxrls: $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(RELABEL_SEQ_OBJ)
+ @echo 'building pxrls'
+- $(CXX) $(CXXFLAGS) -o "pxrls" $(OPT_FLAGS) $(RELABEL_SEQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxrls" $(OPT_FLAGS) $(RELABEL_SEQ_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxrlt: $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(RELABEL_TREE_OBJ)
+ @echo 'building pxrlt'
+- $(CXX) $(CXXFLAGS) -o "pxrlt" $(OPT_FLAGS) $(RELABEL_TREE_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxrlt" $(OPT_FLAGS) $(RELABEL_TREE_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxupgma: $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(UPGMA_OBJ)
+ @echo 'building pxupgma'
+- $(CXX) $(CXXFLAGS) -o "pxupgma" $(OPT_FLAGS) $(UPGMA_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxupgma" $(OPT_FLAGS) $(UPGMA_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+ pxnj: $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS) $(NJ_OBJ)
+ @echo 'building pxnj'
+- $(CXX) $(CXXFLAGS) -o "pxnj" $(OPT_FLAGS) $(NJ_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS)
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o "pxnj" $(OPT_FLAGS) $(NJ_OBJ) $(CPP_OBJS) $(SEQ_OBJS) $(TREE_OBJS)
+ cat man/$@.1.in > man/$@.1
+
+
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,5 @@
build-more-programs.patch
i386.patch
deoptimize.patch
+whatis.patch
+hardening.patch
=====================================
debian/patches/whatis.patch
=====================================
@@ -0,0 +1,557 @@
+Description: fix numerous useless whatis entries.
+ Note however this is not 100% ideal in the current form, as we are patching
+ normally autogenerated files by html2man, in particular using the script
+ provided by upstream: src/generate_manpages.py. If this has to be forwarded
+ upstream, then this would need further adjustment; e.g. a dictionary mapping
+ commands with their description in the script would help with automating the
+ production of the descriptions.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2023-08-15
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- phyx.orig/src/man/pxaa2cdn.1.in
++++ phyx/src/man/pxaa2cdn.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXAA2CDN "1" "July 2023" "pxaa2cdn 1.3" "User Commands"
+ .SH NAME
+-pxaa2cdn \- manual page for pxaa2cdn 1.3
++pxaa2cdn \- generate codon alignment from aligned amino acids and unaligned nucleotides
+ .SH SYNOPSIS
+ .B pxaa2cdn
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxbdfit.1.in
++++ phyx/src/man/pxbdfit.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXBDFIT "1" "July 2023" "pxbdfit 1.3" "User Commands"
+ .SH NAME
+-pxbdfit \- manual page for pxbdfit 1.3
++pxbdfit \- fit lineage diversification model to a tree
+ .SH SYNOPSIS
+ .B pxbdfit
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxbdsim.1.in
++++ phyx/src/man/pxbdsim.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXBDSIM "1" "July 2023" "pxbdsim 1.3" "User Commands"
+ .SH NAME
+-pxbdsim \- manual page for pxbdsim 1.3
++pxbdsim \- birth\-death tree simulator
+ .SH SYNOPSIS
+ .B pxbdsim
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxboot.1.in
++++ phyx/src/man/pxboot.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXBOOT "1" "July 2023" "pxboot 1.3" "User Commands"
+ .SH NAME
+-pxboot \- manual page for pxboot 1.3
++pxboot \- sequence alignment bootstrap or jackknife resampling
+ .SH SYNOPSIS
+ .B pxboot
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxbp.1.in
++++ phyx/src/man/pxbp.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXBP "1" "July 2023" "pxbp 1.3" "User Commands"
+ .SH NAME
+-pxbp \- manual page for pxbp 1.3
++pxbp \- print out bipartitions found in treefiles
+ .SH SYNOPSIS
+ .B pxbp
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxcat.1.in
++++ phyx/src/man/pxcat.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXCAT "1" "July 2023" "pxcat 1.3" "User Commands"
+ .SH NAME
+-pxcat \- manual page for pxcat 1.3
++pxcat \- sequence file concatenation
+ .SH SYNOPSIS
+ .B pxcat
+ [\fI\,OPTIONS\/\fR]... \fI\,FILES\/\fR
+--- phyx.orig/src/man/pxclsq.1.in
++++ phyx/src/man/pxclsq.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXCLSQ "1" "July 2023" "pxclsq 1.3" "User Commands"
+ .SH NAME
+-pxclsq \- manual page for pxclsq 1.3
++pxclsq \- clean positions or taxa with too much ambiguous data
+ .SH SYNOPSIS
+ .B pxclsq
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxcltr.1.in
++++ phyx/src/man/pxcltr.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXCLTR "1" "July 2023" "pxcltr 1.3" "User Commands"
+ .SH NAME
+-pxcltr \- manual page for pxcltr 1.3
++pxcltr \- general tree cleaner
+ .SH SYNOPSIS
+ .B pxcltr
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxcolt.1.in
++++ phyx/src/man/pxcolt.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXCOLT "1" "July 2023" "pxcolt 1.3" "User Commands"
+ .SH NAME
+-pxcolt \- manual page for pxcolt 1.3
++pxcolt \- collapse edges with support below some threshold
+ .SH SYNOPSIS
+ .B pxcolt
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxcomp.1.in
++++ phyx/src/man/pxcomp.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXCOMP "1" "July 2023" "pxcomp 1.3" "User Commands"
+ .SH NAME
+-pxcomp \- manual page for pxcomp 1.3
++pxcomp \- sequence compositional homogeneity test
+ .SH SYNOPSIS
+ .B pxcomp
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxconsq.1.in
++++ phyx/src/man/pxconsq.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXCONSQ "1" "July 2023" "pxconsq 1.3" "User Commands"
+ .SH NAME
+-pxconsq \- manual page for pxconsq 1.3
++pxconsq \- compute consensus sequence from an alignment
+ .SH SYNOPSIS
+ .B pxconsq
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxcontrates.1.in
++++ phyx/src/man/pxcontrates.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXCONTRATES "1" "July 2023" "pxcontrates 1.3" "User Commands"
+ .SH NAME
+-pxcontrates \- manual page for pxcontrates 1.3
++pxcontrates \- continuous character rate estimation with Brownian and OU
+ .SH SYNOPSIS
+ .B pxcontrates
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxfqfilt.1.in
++++ phyx/src/man/pxfqfilt.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXFQFILT "1" "July 2023" "pxfqfilt 1.3" "User Commands"
+ .SH NAME
+-pxfqfilt \- manual page for pxfqfilt 1.3
++pxfqfilt \- filter fastq files by mean quality
+ .SH SYNOPSIS
+ .B pxfqfilt
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxlog.1.in
++++ phyx/src/man/pxlog.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXLOG "1" "July 2023" "pxlog 1.3" "User Commands"
+ .SH NAME
+-pxlog \- manual page for pxlog 1.3
++pxlog \- MCMC log file manipulator
+ .SH SYNOPSIS
+ .B pxlog
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxlssq.1.in
++++ phyx/src/man/pxlssq.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXLSSQ "1" "July 2023" "pxlssq 1.3" "User Commands"
+ .SH NAME
+-pxlssq \- manual page for pxlssq 1.3
++pxlssq \- print sequence file summary
+ .SH SYNOPSIS
+ .B pxlssq
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxlstr.1.in
++++ phyx/src/man/pxlstr.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXLSTR "1" "July 2023" "pxlstr 1.3" "User Commands"
+ .SH NAME
+-pxlstr \- manual page for pxlstr 1.3
++pxlstr \- print tree summary
+ .SH SYNOPSIS
+ .B pxlstr
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxmono.1.in
++++ phyx/src/man/pxmono.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXMONO "1" "July 2023" "pxmono 1.3" "User Commands"
+ .SH NAME
+-pxmono \- manual page for pxmono 1.3
++pxmono \- monophyly checker
+ .SH SYNOPSIS
+ .B pxmono
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxmrca.1.in
++++ phyx/src/man/pxmrca.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXMRCA "1" "July 2023" "pxmrca 1.3" "User Commands"
+ .SH NAME
+-pxmrca \- manual page for pxmrca 1.3
++pxmrca \- get number of descendant tips of internal nodes by mrca statements
+ .SH SYNOPSIS
+ .B pxmrca
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxmrcacut.1.in
++++ phyx/src/man/pxmrcacut.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXMRCACUT "1" "July 2023" "pxmrcacut 1.3" "User Commands"
+ .SH NAME
+-pxmrcacut \- manual page for pxmrcacut 1.3
++pxmrcacut \- extract subclades from trees
+ .SH SYNOPSIS
+ .B pxmrcacut
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxmrcaname.1.in
++++ phyx/src/man/pxmrcaname.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXMRCANAME "1" "July 2023" "pxmrcaname 1.3" "User Commands"
+ .SH NAME
+-pxmrcaname \- manual page for pxmrcaname 1.3
++pxmrcaname \- label internal nodes with clade names
+ .SH SYNOPSIS
+ .B pxmrcaname
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxnj.1.in
++++ phyx/src/man/pxnj.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6.
+ .TH PXNJ "1" "June 2021" "pxnj 1.2" "User Commands"
+ .SH NAME
+-pxnj \- manual page for pxnj 1.2
++pxnj \- basic neighbour\-joining tree maker
+ .SH SYNOPSIS
+ .B pxnj
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxnw.1.in
++++ phyx/src/man/pxnw.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXNW "1" "July 2023" "pxnw 1.3" "User Commands"
+ .SH NAME
+-pxnw \- manual page for pxnw 1.3
++pxnw \- conduct Needleman\-Wunsch analysis for all the seqs in a file
+ .SH SYNOPSIS
+ .B pxnw
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxpoly.1.in
++++ phyx/src/man/pxpoly.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXPOLY "1" "July 2023" "pxpoly 1.3" "User Commands"
+ .SH NAME
+-pxpoly \- manual page for pxpoly 1.3
++pxpoly \- randomly sample polytomies to generate a binary tree
+ .SH SYNOPSIS
+ .B pxpoly
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxrecode.1.in
++++ phyx/src/man/pxrecode.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXRECODE "1" "July 2023" "pxrecode 1.3" "User Commands"
+ .SH NAME
+-pxrecode \- manual page for pxrecode 1.3
++pxrecode \- nucleotide sequence recoding
+ .SH SYNOPSIS
+ .B pxrecode
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxrevcomp.1.in
++++ phyx/src/man/pxrevcomp.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXREVCOMP "1" "July 2023" "pxrevcomp 1.3" "User Commands"
+ .SH NAME
+-pxrevcomp \- manual page for pxrevcomp 1.3
++pxrevcomp \- reverse complement sequences
+ .SH SYNOPSIS
+ .B pxrevcomp
+ [\fI\,OPTIONS\/\fR]... [\fI\,FILE\/\fR]...
+--- phyx.orig/src/man/pxrls.1.in
++++ phyx/src/man/pxrls.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXRLS "1" "July 2023" "pxrls 1.3" "User Commands"
+ .SH NAME
+-pxrls \- manual page for pxrls 1.3
++pxrls \- taxon relabelling from alignments
+ .SH SYNOPSIS
+ .B pxrls
+ [\fI\,OPTIONS\/\fR]... \fI\,FILES\/\fR
+--- phyx.orig/src/man/pxrlt.1.in
++++ phyx/src/man/pxrlt.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXRLT "1" "July 2023" "pxrlt 1.3" "User Commands"
+ .SH NAME
+-pxrlt \- manual page for pxrlt 1.3
++pxrlt \- taxon relabelling for trees
+ .SH SYNOPSIS
+ .B pxrlt
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxrmk.1.in
++++ phyx/src/man/pxrmk.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXRMK "1" "July 2023" "pxrmk 1.3" "User Commands"
+ .SH NAME
+-pxrmk \- manual page for pxrmk 1.3
++pxrmk \- remove two\-degree internal nodes from a tree
+ .SH SYNOPSIS
+ .B pxrmk
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxrms.1.in
++++ phyx/src/man/pxrms.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXRMS "1" "July 2023" "pxrms 1.3" "User Commands"
+ .SH NAME
+-pxrms \- manual page for pxrms 1.3
++pxrms \- remove sequences by label
+ .SH SYNOPSIS
+ .B pxrms
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxrmt.1.in
++++ phyx/src/man/pxrmt.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXRMT "1" "July 2023" "pxrmt 1.3" "User Commands"
+ .SH NAME
+-pxrmt \- manual page for pxrmt 1.3
++pxrmt \- remove tree tips by label
+ .SH SYNOPSIS
+ .B pxrmt
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxrr.1.in
++++ phyx/src/man/pxrr.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXRR "1" "July 2023" "pxrr 1.3" "User Commands"
+ .SH NAME
+-pxrr \- manual page for pxrr 1.3
++pxrr \- reroot (or unroot) a tree file and produce a newick
+ .SH SYNOPSIS
+ .B pxrr
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxs2fa.1.in
++++ phyx/src/man/pxs2fa.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXS2FA "1" "July 2023" "pxs2fa 1.3" "User Commands"
+ .SH NAME
+-pxs2fa \- manual page for pxs2fa 1.3
++pxs2fa \- convert seqfiles from nexus, phylip, fastq to fasta
+ .SH SYNOPSIS
+ .B pxs2fa
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxs2nex.1.in
++++ phyx/src/man/pxs2nex.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXS2NEX "1" "July 2023" "pxs2nex 1.3" "User Commands"
+ .SH NAME
+-pxs2nex \- manual page for pxs2nex 1.3
++pxs2nex \- convert seqfiles from nexus, phylip, or fastq to nexus
+ .SH SYNOPSIS
+ .B pxs2nex
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxs2phy.1.in
++++ phyx/src/man/pxs2phy.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXS2PHY "1" "July 2023" "pxs2phy 1.3" "User Commands"
+ .SH NAME
+-pxs2phy \- manual page for pxs2phy 1.3
++pxs2phy \- convert seqfiles from nexus, phylip, or fastq to phylip
+ .SH SYNOPSIS
+ .B pxs2phy
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxseqgen.1.in
++++ phyx/src/man/pxseqgen.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXSEQGEN "1" "July 2023" "pxseqgen 1.3" "User Commands"
+ .SH NAME
+-pxseqgen \- manual page for pxseqgen 1.3
++pxseqgen \- sequence simulator under the GTR model
+ .SH SYNOPSIS
+ .B pxseqgen
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxssort.1.in
++++ phyx/src/man/pxssort.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXSSORT "1" "July 2023" "pxssort 1.3" "User Commands"
+ .SH NAME
+-pxssort \- manual page for pxssort 1.3
++pxssort \- sort sequences by id or length
+ .SH SYNOPSIS
+ .B pxssort
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxsstat.1.in
++++ phyx/src/man/pxsstat.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXSSTAT "1" "July 2023" "pxsstat 1.3" "User Commands"
+ .SH NAME
+-pxsstat \- manual page for pxsstat 1.3
++pxsstat \- calculate multinomial alignment test statistics
+ .SH SYNOPSIS
+ .B pxsstat
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxstrec.1.in
++++ phyx/src/man/pxstrec.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXSTREC "1" "July 2023" "pxstrec 1.3" "User Commands"
+ .SH NAME
+-pxstrec \- manual page for pxstrec 1.3
++pxstrec \- conduct state reconstruction analyses
+ .SH SYNOPSIS
+ .B pxstrec
+ [\fI\,OPTIONS\/\fR]... \fI\,FILES\/\fR
+--- phyx.orig/src/man/pxsw.1.in
++++ phyx/src/man/pxsw.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXSW "1" "July 2023" "pxsw 1.3" "User Commands"
+ .SH NAME
+-pxsw \- manual page for pxsw 1.3
++pxsw \- conduct Smith\-Waterman analysis for all seqs in a file
+ .SH SYNOPSIS
+ .B pxsw
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxt2new.1.in
++++ phyx/src/man/pxt2new.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXT2NEW "1" "July 2023" "pxt2new 1.3" "User Commands"
+ .SH NAME
+-pxt2new \- manual page for pxt2new 1.3
++pxt2new \- convert from tree file to newick format
+ .SH SYNOPSIS
+ .B pxt2new
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxt2nex.1.in
++++ phyx/src/man/pxt2nex.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXT2NEX "1" "July 2023" "pxt2nex 1.3" "User Commands"
+ .SH NAME
+-pxt2nex \- manual page for pxt2nex 1.3
++pxt2nex \- convert from tree file to vanilla Nexus format
+ .SH SYNOPSIS
+ .B pxt2nex
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxtcol.1.in
++++ phyx/src/man/pxtcol.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXTCOL "1" "July 2023" "pxtcol 1.3" "User Commands"
+ .SH NAME
+-pxtcol \- manual page for pxtcol 1.3
++pxtcol \- add information to color edges of a tree
+ .SH SYNOPSIS
+ .B pxtcol
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxtcomb.1.in
++++ phyx/src/man/pxtcomb.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXTCOMB "1" "July 2023" "pxtcomb 1.3" "User Commands"
+ .SH NAME
+-pxtcomb \- manual page for pxtcomb 1.3
++pxtcomb \- combine set of trees from files
+ .SH SYNOPSIS
+ .B pxtcomb
+ [\fI\,OPTIONS\/\fR]... \fI\,FILE\/\fR
+--- phyx.orig/src/man/pxtgen.1.in
++++ phyx/src/man/pxtgen.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXTGEN "1" "July 2023" "pxtgen 1.3" "User Commands"
+ .SH NAME
+-pxtgen \- manual page for pxtgen 1.3
++pxtgen \- generate all tree topologies for n taxa
+ .SH SYNOPSIS
+ .B pxtgen
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxtlate.1.in
++++ phyx/src/man/pxtlate.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXTLATE "1" "July 2023" "pxtlate 1.3" "User Commands"
+ .SH NAME
+-pxtlate \- manual page for pxtlate 1.3
++pxtlate \- translate DNA alignment to amino acids
+ .SH SYNOPSIS
+ .B pxtlate
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxtrt.1.in
++++ phyx/src/man/pxtrt.1.in
+@@ -1,12 +1,12 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXTRT "1" "July 2023" "pxtrt 1.3" "User Commands"
+ .SH NAME
+-pxtrt \- manual page for pxtrt 1.3
++pxtrt \- trace big tree from taxon list and produce newick
+ .SH SYNOPSIS
+ .B pxtrt
+ [\fI\,OPTIONS\/\fR]...
+ .SH DESCRIPTION
+-This will trace a big tree given a taxon list and and produce newick.
++This will trace a big tree given a taxon list and produce newick.
+ Data can be read from a file or STDIN.
+ .SH OPTIONS
+ .TP
+--- phyx.orig/src/man/pxtscale.1.in
++++ phyx/src/man/pxtscale.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXTSCALE "1" "July 2023" "pxtscale 1.3" "User Commands"
+ .SH NAME
+-pxtscale \- manual page for pxtscale 1.3
++pxtscale \- tree rescaling by factor or root height
+ .SH SYNOPSIS
+ .B pxtscale
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxupgma.1.in
++++ phyx/src/man/pxupgma.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6.
+ .TH PXUPGMA "1" "June 2021" "pxupgma 1.2" "User Commands"
+ .SH NAME
+-pxupgma \- manual page for pxupgma 1.2
++pxupgma \- UPGMA tree generator
+ .SH SYNOPSIS
+ .B pxupgma
+ [\fI\,OPTIONS\/\fR]...
+--- phyx.orig/src/man/pxvcf2fa.1.in
++++ phyx/src/man/pxvcf2fa.1.in
+@@ -1,7 +1,7 @@
+ .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.1.
+ .TH PXVCF2FA "1" "July 2023" "pxvcf2fa 1.3" "User Commands"
+ .SH NAME
+-pxvcf2fa \- manual page for pxvcf2fa 1.3
++pxvcf2fa \- convert vcf file to fasta
+ .SH SYNOPSIS
+ .B pxvcf2fa
+ [\fI\,OPTIONS\/\fR]...
View it on GitLab: https://salsa.debian.org/med-team/phyx/-/compare/d2d4a82357a8e036d6042f8529fa66a56e504de3...3fce76be44c7659df462e0762391993ce4e45bd7
--
View it on GitLab: https://salsa.debian.org/med-team/phyx/-/compare/d2d4a82357a8e036d6042f8529fa66a56e504de3...3fce76be44c7659df462e0762391993ce4e45bd7
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