update deprecated matplotlib calls

Commit also fixes deprecated pandas usage.

CHANGES.md

@@ -1,5 +1,10 @@
 # CHANGES.md
 
+## v0.2.0.13
+
+- fix pandas API call: sort_index() now requires the axis keyword
+- change deprecated matplotlib register_colormap() to matplotlib.colormaps.register()
+
 ## v0.2.12
 
 - fix Issue #177: input filenames that contain an open or a closed parenthesis produce the message: 'WARNING: At least one BLAST run failed. ANIb may fail.'

Makefile

@@ -41,15 +41,15 @@ sge : clean test_sge
 
 ANIm :
 	@echo "Testing ANIm analysis..."
-	./average_nucleotide_identity.py -i $(DATA) -o $(OUT_M) \
+	average_nucleotide_identity.py -i $(DATA) -o $(OUT_M) \
 	  -m ANIm --classes $(CLASSES) --labels $(LABELS) -g -v \
 	  $(LAZYMUMMER) --gformat $(GFORMAT) --gmethod $(GMETHOD)
 	@echo "ANIm analysis test done"
 	@echo
 
 ANIm_sge :
 	@echo "Testing ANIm analysis with SGE..."
-	./average_nucleotide_identity.py -i $(DATA) -o $(OUT_M) \
+	average_nucleotide_identity.py -i $(DATA) -o $(OUT_M) \
 	  -m ANIm --classes $(CLASSES) --labels $(LABELS) -g -v \
 	  --scheduler SGE $(LAZYMUMMER) --gformat $(GFORMAT)\
 	  --gmethod $(GMETHOD)
@@ -58,15 +58,15 @@ ANIm_sge :
 
 ANIb :
 	@echo "Testing ANIb analysis..."
-	./average_nucleotide_identity.py -i $(DATA) -o $(OUT_B) \
+	average_nucleotide_identity.py -i $(DATA) -o $(OUT_B) \
 	  -m ANIb --classes $(CLASSES) --labels $(LABELS) -g -v \
 	  $(LAZYBLAST) --gformat $(GFORMAT) --gmethod $(GMETHOD)
 	@echo "ANIb analysis test done"
 	@echo
 
 ANIb_sge :
 	@echo "Testing ANIb analysis with SGE..."
-	./average_nucleotide_identity.py -i $(DATA) -o $(OUT_B) \
+	average_nucleotide_identity.py -i $(DATA) -o $(OUT_B) \
 	  -m ANIb --classes $(CLASSES) --labels $(LABELS) -g -v \
 	  --scheduler SGE $(LAZYBLAST) --gformat $(GFORMAT) \
 	  --gmethod $(GMETHOD)
@@ -83,7 +83,7 @@ ANIblastall :
 
 ANIblastall_sge :
 	@echo "Testing ANIblastall analysis with SGE..."
-	./average_nucleotide_identity.py -i $(DATA) -o $(OUT_BLASTALL) \
+	average_nucleotide_identity.py -i $(DATA) -o $(OUT_BLASTALL) \
 	  -m ANIblastall --classes $(CLASSES) --labels $(LABELS) -g -v \
 	  --scheduler SGE $(LAZYBLAST) --gformat $(GFORMAT)
 	  --gmethod $(GMETHOD)
@@ -94,7 +94,7 @@ BLAST : ANIb ANIblastall
 
 TETRA :
 	@echo "Testing TETRA analysis..."
-	./average_nucleotide_identity.py -i $(DATA) -o $(OUT_TETRA) \
+	average_nucleotide_identity.py -i $(DATA) -o $(OUT_TETRA) \
 	  -m TETRA --classes $(CLASSES) --labels $(LABELS) -g -v \
 	  $(LAZYTETRA) --gformat $(GFORMAT) --gmethod $(GMETHOD)
 	@echo "TETRA analysis test done"

pyani/pyani_graphics.py

@@ -67,14 +67,13 @@
 
 
 # Register Matplotlib colourmaps
-plt.register_cmap(cmap=pyani_config.CMAP_SPBND_BURD)
-plt.register_cmap(cmap=pyani_config.CMAP_HADAMARD_BURD)
-plt.register_cmap(cmap=pyani_config.CMAP_BURD)
+plt.colormaps.register(cmap=pyani_config.CMAP_SPBND_BURD)
+plt.colormaps.register(cmap=pyani_config.CMAP_HADAMARD_BURD)
+plt.colormaps.register(cmap=pyani_config.CMAP_BURD)
 
 
 # Convenience class to hold heatmap graphics parameters
 class Params(object):  # pylint: disable=too-few-public-methods
-
     """Convenience class to hold heatmap rendering parameters."""
 
     def __init__(self, params, labels=None, classes=None):
@@ -116,9 +115,7 @@ def get_seaborn_colorbar(dfr, classes):
         lvl: pal
         for (lvl, pal) in zip(
             levels,
-            sns.cubehelix_palette(
-                len(levels), light=0.9, dark=0.1, reverse=True, start=1, rot=-2
-            ),
+            sns.cubehelix_palette(len(levels), light=0.9, dark=0.1, reverse=True, start=1, rot=-2),
         )
     }
     lvl_pal = {cls: paldict[lvl] for (cls, lvl) in list(classes.items())}
@@ -326,9 +323,7 @@ def add_mpl_colorscale(fig, heatmap_gs, ax_map, params, title=None):
         exponent = int(floor(log10(params.vmax))) - 1
         cbticks = [int(round(e, -exponent)) for e in cbticks]
 
-    scale_subplot = gridspec.GridSpecFromSubplotSpec(
-        1, 3, subplot_spec=heatmap_gs[0, 0], wspace=0.0, hspace=0.0
-    )
+    scale_subplot = gridspec.GridSpecFromSubplotSpec(1, 3, subplot_spec=heatmap_gs[0, 0], wspace=0.0, hspace=0.0)
     scale_ax = fig.add_subplot(scale_subplot[0, 1])
     cbar = fig.colorbar(ax_map, scale_ax, ticks=cbticks)
     if title:
@@ -358,9 +353,7 @@ def heatmap_mpl(dfr, outfilename=None, title=None, params=None):
     fig = plt.figure(figsize=(figsize, figsize))
     # if title:
     #     fig.suptitle(title)
-    heatmap_gs = gridspec.GridSpec(
-        2, 2, wspace=0.0, hspace=0.0, width_ratios=[0.3, 1], height_ratios=[0.3, 1]
-    )
+    heatmap_gs = gridspec.GridSpec(2, 2, wspace=0.0, hspace=0.0, width_ratios=[0.3, 1], height_ratios=[0.3, 1])
 
     # Add column and row dendrograms/axes to figure
     coldend = add_mpl_dendrogram(dfr, fig, heatmap_gs, orientation="col")

tests/test_anib.py

@@ -62,17 +62,14 @@
 
 
 class TestBLASTCmdline(unittest.TestCase):
-
     """Class defining tests of BLAST command-line generation."""
 
     def setUp(self):
         """Set parameters for tests."""
         self.indir = os.path.join("tests", "test_input", "anib")
         self.outdir = os.path.join("tests", "test_output", "anib")
         self.seqdir = os.path.join("tests", "test_input", "sequences")
-        self.infiles = [
-            os.path.join(self.seqdir, fname) for fname in os.listdir(self.seqdir)
-        ]
+        self.infiles = [os.path.join(self.seqdir, fname) for fname in os.listdir(self.seqdir)]
         self.fraglen = 1000
         self.fmtdboutdir = os.path.join(self.outdir, "formatdb")
         self.fmtdbcmd = " ".join(
@@ -88,15 +85,10 @@ def setUp(self):
                 "makeblastdb -dbtype nucl -in",
                 "tests/test_input/sequences/NC_002696.fna",
                 "-title NC_002696 -out",
-                os.path.join(
-                    "tests", "test_output", "anib", "makeblastdb", "NC_002696.fna"
-                ),
+                os.path.join("tests", "test_output", "anib", "makeblastdb", "NC_002696.fna"),
             ]
         )
-        self.blastdbfnames = [
-            os.path.join(self.seqdir, fname)
-            for fname in ("NC_002696.fna", "NC_010338.fna")
-        ]
+        self.blastdbfnames = [os.path.join(self.seqdir, fname) for fname in ("NC_002696.fna", "NC_010338.fna")]
         self.blastdbtgt = [
             (
                 " ".join(
@@ -146,9 +138,7 @@ def setUp(self):
         self.blastncmd = " ".join(
             [
                 "blastn -out",
-                os.path.join(
-                    "tests", "test_output", "anib", "NC_002696_vs_NC_010338.blast_tab"
-                ),
+                os.path.join("tests", "test_output", "anib", "NC_002696_vs_NC_010338.blast_tab"),
                 "-query tests/test_input/sequences/NC_002696.fna",
                 "-db tests/test_input/sequences/NC_010338.fna",
                 "-xdrop_gap_final 150 -dust no -evalue 1e-15",
@@ -160,9 +150,7 @@ def setUp(self):
         self.blastallcmd = " ".join(
             [
                 "blastall -p blastn -o",
-                os.path.join(
-                    "tests", "test_output", "anib", "NC_002696_vs_NC_010338.blast_tab"
-                ),
+                os.path.join("tests", "test_output", "anib", "NC_002696_vs_NC_010338.blast_tab"),
                 "-i tests/test_input/sequences/NC_002696.fna",
                 "-d tests/test_input/sequences/NC_010338.fna",
                 "-X 150 -q -1 -F F -e 1e-15 -b 1 -v 1 -m 8",
@@ -266,23 +254,19 @@ def setUp(self):
             [
                 (
                     "tests/test_output/anib/NC_002696.fna",
-                    "formatdb -p F -i tests/test_output/anib/NC_002696.fna "
-                    + "-t NC_002696",
+                    "formatdb -p F -i tests/test_output/anib/NC_002696.fna " + "-t NC_002696",
                 ),
                 (
                     "tests/test_output/anib/NC_010338.fna",
-                    "formatdb -p F -i tests/test_output/anib/NC_010338.fna "
-                    + "-t NC_010338",
+                    "formatdb -p F -i tests/test_output/anib/NC_010338.fna " + "-t NC_010338",
                 ),
                 (
                     "tests/test_output/anib/NC_011916.fna",
-                    "formatdb -p F -i tests/test_output/anib/NC_011916.fna "
-                    + "-t NC_011916",
+                    "formatdb -p F -i tests/test_output/anib/NC_011916.fna " + "-t NC_011916",
                 ),
                 (
                     "tests/test_output/anib/NC_014100.fna",
-                    "formatdb -p F -i tests/test_output/anib/NC_014100.fna "
-                    + "-t NC_014100",
+                    "formatdb -p F -i tests/test_output/anib/NC_014100.fna " + "-t NC_014100",
                 ),
             ]
         )
@@ -293,83 +277,63 @@ def setUp(self):
     @nottest  #  legacy BLAST deprecated
     def test_formatdb_generation(self):
         """generate formatdb command-line."""
-        cmd = anib.construct_formatdb_cmd(
-            os.path.join(self.seqdir, "NC_002696.fna"), self.fmtdboutdir
-        )
+        cmd = anib.construct_formatdb_cmd(os.path.join(self.seqdir, "NC_002696.fna"), self.fmtdboutdir)
         assert_equal(cmd[0], self.fmtdbcmd)  # correct command
         assert os.path.isfile(cmd[1])  # creates new file
 
     def test_makeblastdb_generation(self):
         """generate makeblastdb command-line."""
-        cmd = anib.construct_makeblastdb_cmd(
-            os.path.join(self.seqdir, "NC_002696.fna"), self.makeblastdbdir
-        )
+        cmd = anib.construct_makeblastdb_cmd(os.path.join(self.seqdir, "NC_002696.fna"), self.makeblastdbdir)
         assert_equal(cmd[0], self.makeblastdbcmd)  # correct command
 
     def test_blastdb_commands(self):
         """generate BLAST+ db commands."""
         # BLAST+
-        cmds = anib.generate_blastdb_commands(
-            self.blastdbfnames, self.outdir, mode="ANIb"
-        )
+        cmds = anib.generate_blastdb_commands(self.blastdbfnames, self.outdir, mode="ANIb")
         assert_equal(cmds, self.blastdbtgt)
 
     @nottest  #  legacy BLAST deprecated
     def test_legacy_blastdb_commands(self):
         """generate legacy BLAST db commands."""
         # legacy
-        cmds = anib.generate_blastdb_commands(
-            self.blastdbfnames, self.outdir, mode="ANIblastall"
-        )
+        cmds = anib.generate_blastdb_commands(self.blastdbfnames, self.outdir, mode="ANIblastall")
         assert_equal(cmds, self.blastdbtgtlegacy)
 
     def test_blastn_generation(self):
         """generate BLASTN+ command-line."""
-        cmd = anib.construct_blastn_cmdline(
-            self.blastdbfnames[0], self.blastdbfnames[1], self.outdir
-        )
+        cmd = anib.construct_blastn_cmdline(self.blastdbfnames[0], self.blastdbfnames[1], self.outdir)
         assert_equal(cmd, self.blastncmd)
 
     @nottest  #  legacy BLAST deprecated
     def test_blastall_generation(self):
         """generate legacy BLASTN command-line."""
-        cmd = anib.construct_blastall_cmdline(
-            self.blastdbfnames[0], self.blastdbfnames[1], self.outdir
-        )
+        cmd = anib.construct_blastall_cmdline(self.blastdbfnames[0], self.blastdbfnames[1], self.outdir)
         assert_equal(cmd, self.blastallcmd)
 
     def test_blastn_commands(self):
         """generate BLASTN+ commands."""
         # BLAST+
-        cmds = anib.generate_blastn_commands(
-            self.blastdbfnames, self.outdir, mode="ANIb"
-        )
+        cmds = anib.generate_blastn_commands(self.blastdbfnames, self.outdir, mode="ANIb")
         assert_equal(cmds, self.blastntgt)
 
     @nottest  #  legacy BLAST deprecated
     def test_legacy_blastn_commands(self):
         """generate legacy BLASTN commands."""
-        cmds = anib.generate_blastn_commands(
-            self.blastdbfnames, self.outdir, mode="ANIblastall"
-        )
+        cmds = anib.generate_blastn_commands(self.blastdbfnames, self.outdir, mode="ANIblastall")
         assert_equal(cmds, self.blastalltgt)
 
     @nottest  #  legacy BLAST deprecated
     def test_blastall_dbjobdict(self):
         """generate dictionary of legacy BLASTN database jobs."""
         blastcmds = anib.make_blastcmd_builder("ANIblastall", self.outdir)
         jobdict = anib.build_db_jobs(self.infiles, blastcmds)
-        assert_equal(
-            sorted([(k, v.script) for (k, v) in jobdict.items()]), self.blastalljobdict
-        )
+        assert_equal(sorted([(k, v.script) for (k, v) in jobdict.items()]), self.blastalljobdict)
 
     def test_blastn_dbjobdict(self):
         """generate dictionary of BLASTN+ database jobs."""
         blastcmds = anib.make_blastcmd_builder("ANIb", self.outdir)
         jobdict = anib.build_db_jobs(self.infiles, blastcmds)
-        assert_equal(
-            sorted([(k, v.script) for (k, v) in jobdict.items()]), self.blastnjobdict
-        )
+        assert_equal(sorted([(k, v.script) for (k, v) in jobdict.items()]), self.blastnjobdict)
 
     def test_blastn_graph(self):
         """create jobgraph for BLASTN+ jobs."""
@@ -400,7 +364,6 @@ def test_blastall_graph(self):
 
 
 class TestFragments(unittest.TestCase):
-
     """Class defining tests of ANIb FASTA fragmentation"""
 
     def setUp(self):
@@ -442,7 +405,6 @@ def test_fragment_files(self):
 
 
 class TestParsing(unittest.TestCase):
-
     """Class defining tests of BLAST output parsing."""
 
     def setUp(self):
@@ -502,9 +464,7 @@ def test_parse_blasttab(self):
         result = anib.parse_blast_tab(self.fname, fragdata, 0.3, 0.7, mode="ANIb")
         assert_equal(result, (4016551, 93, 99.997693577050029))
         # ANIblastall output
-        result = anib.parse_blast_tab(
-            self.fname_legacy, fragdata, 0.3, 0.7, mode="ANIblastall"
-        )
+        result = anib.parse_blast_tab(self.fname_legacy, fragdata, 0.3, 0.7, mode="ANIblastall")
         assert_equal(result, (1966922, 406104, 78.578978313253018))
 
     def test_blastdir_processing(self):
@@ -514,8 +474,8 @@ def test_blastdir_processing(self):
         # ANIb
         result = anib.process_blast(self.anibdir, orglengths, fraglengths, mode="ANIb")
         assert_frame_equal(
-            result.percentage_identity.sort_index(1).sort_index(),
-            self.anibtgt.sort_index(1).sort_index(),
+            result.percentage_identity.sort_index(axis=1).sort_index(),
+            self.anibtgt.sort_index(axis=1).sort_index(),
         )
 
     @nottest  #  legacy BLAST deprecated
@@ -524,9 +484,7 @@ def test_legacy_blastdir_processing(self):
         orglengths = pyani_files.get_sequence_lengths(self.infnames)
         fraglengths = anib.get_fraglength_dict(self.fragfiles)
         # ANIblastall
-        result = anib.process_blast(
-            self.aniblastalldir, orglengths, fraglengths, mode="ANIblastall"
-        )
+        result = anib.process_blast(self.aniblastalldir, orglengths, fraglengths, mode="ANIblastall")
         assert_frame_equal(
             result.percentage_identity.sort_index(1).sort_index(),
             self.aniblastalltgt.sort_index(1).sort_index(),

tests/test_anim.py

@@ -63,7 +63,6 @@
 
 
 class TestNUCmerCmdline(unittest.TestCase):
-
     """Class defining tests of NUCmer command-line generation."""
 
     def setUp(self):
@@ -152,16 +151,12 @@ def test_single_cmd_generation(self):
         Tests that a single NUCmer/delta-filter command-line pair is
         produced correctly
         """
-        cmds = anim.construct_nucmer_cmdline(
-            "file1.fna", "file2.fna", outdir=self.outdir
-        )
+        cmds = anim.construct_nucmer_cmdline("file1.fna", "file2.fna", outdir=self.outdir)
         assert_equal(cmds, (self.ntgt, self.ftgt))
 
     def test_maxmatch_cmd_generation(self):
         """generate NUCmer command line with maxmatch."""
-        ncmd, fcmd = anim.construct_nucmer_cmdline(
-            "file1.fna", "file2.fna", outdir=self.outdir, maxmatch=True
-        )
+        ncmd, fcmd = anim.construct_nucmer_cmdline("file1.fna", "file2.fna", outdir=self.outdir, maxmatch=True)
         assert_equal(ncmd, self.ntgtmax)
 
     def test_multi_cmd_generation(self):
@@ -182,13 +177,10 @@ def test_nucmer_job_generation(self):
         for idx, job in enumerate(joblist):
             assert_equal(job.name, "test_%06d-f" % idx)  # filter job name
             assert_equal(len(job.dependencies), 1)  # has NUCmer job
-            assert_equal(
-                job.dependencies[0].name, "test_%06d-n" % idx
-            )  # NUCmer job name
+            assert_equal(job.dependencies[0].name, "test_%06d-n" % idx)  # NUCmer job name
 
 
 class TestDeltafileProcessing(unittest.TestCase):
-
     """Class defining tests for .delta/.filter file parsing"""
 
     def setUp(self):
@@ -219,6 +211,6 @@ def test_process_deltadir(self):
         orglengths = pyani_files.get_sequence_lengths(seqfiles)
         result = anim.process_deltadir(self.deltadir, orglengths)
         assert_frame_equal(
-            result.percentage_identity.sort_index(1).sort_index(),
-            self.df_pid.sort_index(1).sort_index(),
+            result.percentage_identity.sort_index(axis=1).sort_index(),
+            self.df_pid.sort_index(axis=1).sort_index(),
         )