hercules/python/labours/labours.py

#!/usr/bin/env python3
import argparse
import contextlib
from collections import defaultdict, namedtuple
from datetime import datetime, timedelta
from importlib import import_module
import io
from itertools import chain
import json
import os
import re
import shutil
import subprocess
import sys
import tempfile
import threading
import time
import warnings

import tqdm

import numpy
import yaml


if sys.version_info[0] < 3:
    # OK, ancients, I will support Python 2, but you owe me a beer
    input = raw_input  # noqa: F821


def list_matplotlib_styles():
    script = "import sys; from matplotlib import pyplot; " \
             "sys.stdout.write(repr(pyplot.style.available))"
    styles = eval(subprocess.check_output([sys.executable, "-c", script]))
    styles.remove("classic")
    return ["default", "classic"] + styles


def parse_args():
    parser = argparse.ArgumentParser()
    parser.add_argument("-o", "--output", default="",
                        help="Path to the output file/directory (empty for display). "
                             "If the extension is JSON, the data is saved instead of "
                             "the real image.")
    parser.add_argument("-i", "--input", default="-",
                        help="Path to the input file (- for stdin).")
    parser.add_argument("-f", "--input-format", default="auto", choices=["yaml", "pb", "auto"])
    parser.add_argument("--font-size", default=12, type=int,
                        help="Size of the labels and legend.")
    parser.add_argument("--style", default="ggplot", choices=list_matplotlib_styles(),
                        help="Plot style to use.")
    parser.add_argument("--backend", help="Matplotlib backend to use.")
    parser.add_argument("--background", choices=["black", "white"], default="white",
                        help="Plot's general color scheme.")
    parser.add_argument("--size", help="Axes' size in inches, for example \"12,9\"")
    parser.add_argument("--relative", action="store_true",
                        help="Occupy 100%% height for every measurement.")
    parser.add_argument("--tmpdir", help="Temporary directory for intermediate files.")
    parser.add_argument("-m", "--mode", dest="modes", default=[], action="append",
                        choices=["burndown-project", "burndown-file", "burndown-person",
                                 "overwrites-matrix", "ownership", "couples-files",
                                 "couples-people", "couples-shotness", "shotness", "sentiment",
                                 "devs", "devs-efforts", "old-vs-new", "run-times",
                                 "languages", "devs-parallel", "all"],
                        help="What to plot. Can be repeated, e.g. "
                             "-m burndown-project -m run-times")
    parser.add_argument(
        "--resample", default="year",
        help="The way to resample the time series. Possible values are: "
             "\"month\", \"year\", \"no\", \"raw\" and pandas offset aliases ("
             "http://pandas.pydata.org/pandas-docs/stable/timeseries.html"
             "#offset-aliases).")
    dateutil_url = "https://dateutil.readthedocs.io/en/stable/parser.html#dateutil.parser.parse"
    parser.add_argument("--start-date",
                        help="Start date of time-based plots. Any format is accepted which is "
                             "supported by %s" % dateutil_url)
    parser.add_argument("--end-date",
                        help="End date of time-based plots. Any format is accepted which is "
                             "supported by %s" % dateutil_url)
    parser.add_argument("--disable-projector", action="store_true",
                        help="Do not run Tensorflow Projector on couples.")
    parser.add_argument("--max-people", default=20, type=int,
                        help="Maximum number of developers in overwrites matrix and people plots.")
    parser.add_argument("--order-ownership-by-time", action="store_true",
                        help="Sort developers in the ownership plot according to their first "
                             "appearance in the history. The default is sorting by the number of "
                             "commits.")
    args = parser.parse_args()
    return args


class Reader(object):
    def read(self, file):
        raise NotImplementedError

    def get_name(self):
        raise NotImplementedError

    def get_header(self):
        raise NotImplementedError

    def get_burndown_parameters(self):
        raise NotImplementedError

    def get_project_burndown(self):
        raise NotImplementedError

    def get_files_burndown(self):
        raise NotImplementedError

    def get_people_burndown(self):
        raise NotImplementedError

    def get_ownership_burndown(self):
        raise NotImplementedError

    def get_people_interaction(self):
        raise NotImplementedError

    def get_files_coocc(self):
        raise NotImplementedError

    def get_people_coocc(self):
        raise NotImplementedError

    def get_shotness_coocc(self):
        raise NotImplementedError

    def get_shotness(self):
        raise NotImplementedError

    def get_sentiment(self):
        raise NotImplementedError

    def get_devs(self):
        raise NotImplementedError


class YamlReader(Reader):
    def read(self, file):
        yaml.reader.Reader.NON_PRINTABLE = re.compile(r"(?!x)x")
        try:
            loader = yaml.CLoader
        except AttributeError:
            print("Warning: failed to import yaml.CLoader, falling back to slow yaml.Loader")
            loader = yaml.Loader
        try:
            if file != "-":
                with open(file) as fin:
                    data = yaml.load(fin, Loader=loader)
            else:
                data = yaml.load(sys.stdin, Loader=loader)
        except (UnicodeEncodeError, yaml.reader.ReaderError) as e:
            print("\nInvalid unicode in the input: %s\nPlease filter it through "
                  "fix_yaml_unicode.py" % e)
            sys.exit(1)
        if data is None:
            print("\nNo data has been read - has Hercules crashed?")
            sys.exit(1)
        self.data = data

    def get_run_times(self):
        return {}

    def get_name(self):
        return self.data["hercules"]["repository"]

    def get_header(self):
        header = self.data["hercules"]
        return header["begin_unix_time"], header["end_unix_time"]

    def get_burndown_parameters(self):
        header = self.data["Burndown"]
        return header["sampling"], header["granularity"], header["tick_size"]

    def get_project_burndown(self):
        return self.data["hercules"]["repository"], \
            self._parse_burndown_matrix(self.data["Burndown"]["project"]).T

    def get_files_burndown(self):
        return [(p[0], self._parse_burndown_matrix(p[1]).T)
                for p in self.data["Burndown"]["files"].items()]

    def get_people_burndown(self):
        return [(p[0], self._parse_burndown_matrix(p[1]).T)
                for p in self.data["Burndown"]["people"].items()]

    def get_ownership_burndown(self):
        return self.data["Burndown"]["people_sequence"].copy(), \
            {p[0]: self._parse_burndown_matrix(p[1])
             for p in self.data["Burndown"]["people"].items()}

    def get_people_interaction(self):
        return self.data["Burndown"]["people_sequence"].copy(), \
            self._parse_burndown_matrix(self.data["Burndown"]["people_interaction"])

    def get_files_coocc(self):
        coocc = self.data["Couples"]["files_coocc"]
        return coocc["index"], self._parse_coocc_matrix(coocc["matrix"])

    def get_people_coocc(self):
        coocc = self.data["Couples"]["people_coocc"]
        return coocc["index"], self._parse_coocc_matrix(coocc["matrix"])

    def get_shotness_coocc(self):
        shotness = self.data["Shotness"]
        index = ["%s:%s" % (i["file"], i["name"]) for i in shotness]
        indptr = numpy.zeros(len(shotness) + 1, dtype=numpy.int64)
        indices = []
        data = []
        for i, record in enumerate(shotness):
            pairs = [(int(k), v) for k, v in record["counters"].items()]
            pairs.sort()
            indptr[i + 1] = indptr[i] + len(pairs)
            for k, v in pairs:
                indices.append(k)
                data.append(v)
        indices = numpy.array(indices, dtype=numpy.int32)
        data = numpy.array(data, dtype=numpy.int32)
        from scipy.sparse import csr_matrix
        return index, csr_matrix((data, indices, indptr), shape=(len(shotness),) * 2)

    def get_shotness(self):
        from munch import munchify
        obj = munchify(self.data["Shotness"])
        # turn strings into ints
        for item in obj:
            item.counters = {int(k): v for k, v in item.counters.items()}
        if len(obj) == 0:
            raise KeyError
        return obj

    def get_sentiment(self):
        from munch import munchify
        return munchify({int(key): {
            "Comments": vals[2].split("|"),
            "Commits": vals[1],
            "Value": float(vals[0])
        } for key, vals in self.data["Sentiment"].items()})

    def get_devs(self):
        people = self.data["Devs"]["people"]
        days = {int(d): {int(dev): DevDay(*(int(x) for x in day[:-1]), day[-1])
                         for dev, day in devs.items()}
                for d, devs in self.data["Devs"]["ticks"].items()}
        return people, days

    def _parse_burndown_matrix(self, matrix):
        return numpy.array([numpy.fromstring(line, dtype=int, sep=" ")
                            for line in matrix.split("\n")])

    def _parse_coocc_matrix(self, matrix):
        from scipy.sparse import csr_matrix
        data = []
        indices = []
        indptr = [0]
        for row in matrix:
            for k, v in sorted(row.items()):
                data.append(v)
                indices.append(k)
            indptr.append(indptr[-1] + len(row))
        return csr_matrix((data, indices, indptr), shape=(len(matrix),) * 2)


class ProtobufReader(Reader):
    def read(self, file):
        try:
            from labours.pb_pb2 import AnalysisResults
        except ImportError as e:
            print("\n\n>>> You need to generate python/hercules/pb/pb_pb2.py - run \"make\"\n",
                  file=sys.stderr)
            raise e from None
        self.data = AnalysisResults()
        if file != "-":
            with open(file, "rb") as fin:
                bytes = fin.read()
        else:
            bytes = sys.stdin.buffer.read()
        if not bytes:
            raise ValueError("empty input")
        self.data.ParseFromString(bytes)
        self.contents = {}
        for key, val in self.data.contents.items():
            try:
                mod, name = PB_MESSAGES[key].rsplit(".", 1)
            except KeyError:
                sys.stderr.write("Warning: there is no registered PB decoder for %s\n" % key)
                continue
            cls = getattr(import_module(mod), name)
            self.contents[key] = msg = cls()
            msg.ParseFromString(val)

    def get_run_times(self):
        return {key: val for key, val in self.data.header.run_time_per_item.items()}

    def get_name(self):
        return self.data.header.repository

    def get_header(self):
        header = self.data.header
        return header.begin_unix_time, header.end_unix_time

    def get_burndown_parameters(self):
        burndown = self.contents["Burndown"]
        return burndown.sampling, burndown.granularity, burndown.tick_size / 1000000000

    def get_project_burndown(self):
        return self._parse_burndown_matrix(self.contents["Burndown"].project)

    def get_files_burndown(self):
        return [self._parse_burndown_matrix(i) for i in self.contents["Burndown"].files]

    def get_people_burndown(self):
        return [self._parse_burndown_matrix(i) for i in self.contents["Burndown"].people]

    def get_ownership_burndown(self):
        people = self.get_people_burndown()
        return [p[0] for p in people], {p[0]: p[1].T for p in people}

    def get_people_interaction(self):
        burndown = self.contents["Burndown"]
        return [i.name for i in burndown.people], \
            self._parse_sparse_matrix(burndown.people_interaction).toarray()

    def get_files_coocc(self):
        node = self.contents["Couples"].file_couples
        return list(node.index), self._parse_sparse_matrix(node.matrix)

    def get_people_coocc(self):
        node = self.contents["Couples"].people_couples
        return list(node.index), self._parse_sparse_matrix(node.matrix)

    def get_shotness_coocc(self):
        shotness = self.get_shotness()
        index = ["%s:%s" % (i.file, i.name) for i in shotness]
        indptr = numpy.zeros(len(shotness) + 1, dtype=numpy.int32)
        indices = []
        data = []
        for i, record in enumerate(shotness):
            pairs = list(record.counters.items())
            pairs.sort()
            indptr[i + 1] = indptr[i] + len(pairs)
            for k, v in pairs:
                indices.append(k)
                data.append(v)
        indices = numpy.array(indices, dtype=numpy.int32)
        data = numpy.array(data, dtype=numpy.int32)
        from scipy.sparse import csr_matrix
        return index, csr_matrix((data, indices, indptr), shape=(len(shotness),) * 2)

    def get_shotness(self):
        records = self.contents["Shotness"].records
        if len(records) == 0:
            raise KeyError
        return records

    def get_sentiment(self):
        byday = self.contents["Sentiment"].SentimentByDay
        if len(byday) == 0:
            raise KeyError
        return byday

    def get_devs(self):
        people = list(self.contents["Devs"].dev_index)
        days = {d: {dev: DevDay(stats.commits, stats.stats.added, stats.stats.removed,
                                stats.stats.changed, {k: [v.added, v.removed, v.changed]
                                                      for k, v in stats.languages.items()})
                    for dev, stats in day.devs.items()}
                for d, day in self.contents["Devs"].ticks.items()}
        return people, days

    def _parse_burndown_matrix(self, matrix):
        dense = numpy.zeros((matrix.number_of_rows, matrix.number_of_columns), dtype=int)
        for y, row in enumerate(matrix.rows):
            for x, col in enumerate(row.columns):
                dense[y, x] = col
        return matrix.name, dense.T

    def _parse_sparse_matrix(self, matrix):
        from scipy.sparse import csr_matrix
        return csr_matrix((list(matrix.data), list(matrix.indices), list(matrix.indptr)),
                          shape=(matrix.number_of_rows, matrix.number_of_columns))


READERS = {"yaml": YamlReader, "yml": YamlReader, "pb": ProtobufReader}
PB_MESSAGES = {
    "Burndown": "labours.pb_pb2.BurndownAnalysisResults",
    "Couples": "labours.pb_pb2.CouplesAnalysisResults",
    "Shotness": "labours.pb_pb2.ShotnessAnalysisResults",
    "Devs": "labours.pb_pb2.DevsAnalysisResults",
}


def read_input(args):
    sys.stdout.write("Reading the input... ")
    sys.stdout.flush()
    if args.input != "-":
        if args.input_format == "auto":
            try:
                args.input_format = args.input.rsplit(".", 1)[1]
            except IndexError:
                try:
                    with open(args.input) as f:
                        f.read(1 << 16)
                    args.input_format = "yaml"
                except UnicodeDecodeError:
                    args.input_format = "pb"
    elif args.input_format == "auto":
        args.input_format = "yaml"
    reader = READERS[args.input_format]()
    reader.read(args.input)
    print("done")
    return reader


class DevDay(namedtuple("DevDay", ("Commits", "Added", "Removed", "Changed", "Languages"))):
    def add(self, dd):
        langs = defaultdict(lambda: [0] * 3)
        for key, val in self.Languages.items():
            for i in range(3):
                langs[key][i] += val[i]
        for key, val in dd.Languages.items():
            for i in range(3):
                langs[key][i] += val[i]
        return DevDay(Commits=self.Commits + dd.Commits,
                      Added=self.Added + dd.Added,
                      Removed=self.Removed + dd.Removed,
                      Changed=self.Changed + dd.Changed,
                      Languages=dict(langs))


def fit_kaplan_meier(matrix):
    from lifelines import KaplanMeierFitter

    T = []
    W = []
    indexes = numpy.arange(matrix.shape[0], dtype=int)
    entries = numpy.zeros(matrix.shape[0], int)
    dead = set()
    for i in range(1, matrix.shape[1]):
        diff = matrix[:, i - 1] - matrix[:, i]
        entries[diff < 0] = i
        mask = diff > 0
        deaths = diff[mask]
        T.append(numpy.full(len(deaths), i) - entries[indexes[mask]])
        W.append(deaths)
        entered = entries > 0
        entered[0] = True
        dead = dead.union(set(numpy.where((matrix[:, i] == 0) & entered)[0]))
    # add the survivors as censored
    nnzind = entries != 0
    nnzind[0] = True
    nnzind[sorted(dead)] = False
    T.append(numpy.full(nnzind.sum(), matrix.shape[1]) - entries[nnzind])
    W.append(matrix[nnzind, -1])
    T = numpy.concatenate(T)
    E = numpy.ones(len(T), bool)
    E[-nnzind.sum():] = 0
    W = numpy.concatenate(W)
    if T.size == 0:
        return None
    kmf = KaplanMeierFitter().fit(T, E, weights=W)
    return kmf


def print_survival_function(kmf, sampling):
    sf = kmf.survival_function_
    sf.index = [timedelta(days=d) for d in sf.index * sampling]
    sf.columns = ["Ratio of survived lines"]
    try:
        print(sf[len(sf) // 6::len(sf) // 6].append(sf.tail(1)))
    except ValueError:
        pass


def interpolate_burndown_matrix(matrix, granularity, sampling, progress=False):
    daily = numpy.zeros(
        (matrix.shape[0] * granularity, matrix.shape[1] * sampling),
        dtype=numpy.float32)
    """
    ----------> samples, x
    |
    |
    |
    ⌄
    bands, y
    """
    for y in tqdm.tqdm(range(matrix.shape[0]), disable=(not progress)):
        for x in range(matrix.shape[1]):
            if y * granularity > (x + 1) * sampling:
                # the future is zeros
                continue

            def decay(start_index: int, start_val: float):
                if start_val == 0:
                    return
                k = matrix[y][x] / start_val  # <= 1
                scale = (x + 1) * sampling - start_index
                for i in range(y * granularity, (y + 1) * granularity):
                    initial = daily[i][start_index - 1]
                    for j in range(start_index, (x + 1) * sampling):
                        daily[i][j] = initial * (
                            1 + (k - 1) * (j - start_index + 1) / scale)

            def grow(finish_index: int, finish_val: float):
                initial = matrix[y][x - 1] if x > 0 else 0
                start_index = x * sampling
                if start_index < y * granularity:
                    start_index = y * granularity
                if finish_index == start_index:
                    return
                avg = (finish_val - initial) / (finish_index - start_index)
                for j in range(x * sampling, finish_index):
                    for i in range(start_index, j + 1):
                        daily[i][j] = avg
                # copy [x*g..y*s)
                for j in range(x * sampling, finish_index):
                    for i in range(y * granularity, x * sampling):
                        daily[i][j] = daily[i][j - 1]

            if (y + 1) * granularity >= (x + 1) * sampling:
                # x*granularity <= (y+1)*sampling
                # 1. x*granularity <= y*sampling
                #    y*sampling..(y+1)sampling
                #
                #       x+1
                #        /
                #       /
                #      / y+1  -|
                #     /        |
                #    / y      -|
                #   /
                #  / x
                #
                # 2. x*granularity > y*sampling
                #    x*granularity..(y+1)sampling
                #
                #       x+1
                #        /
                #       /
                #      / y+1  -|
                #     /        |
                #    / x      -|
                #   /
                #  / y
                if y * granularity <= x * sampling:
                    grow((x + 1) * sampling, matrix[y][x])
                elif (x + 1) * sampling > y * granularity:
                    grow((x + 1) * sampling, matrix[y][x])
                    avg = matrix[y][x] / ((x + 1) * sampling - y * granularity)
                    for j in range(y * granularity, (x + 1) * sampling):
                        for i in range(y * granularity, j + 1):
                            daily[i][j] = avg
            elif (y + 1) * granularity >= x * sampling:
                # y*sampling <= (x+1)*granularity < (y+1)sampling
                # y*sampling..(x+1)*granularity
                # (x+1)*granularity..(y+1)sampling
                #        x+1
                #         /\
                #        /  \
                #       /    \
                #      /    y+1
                #     /
                #    y
                v1 = matrix[y][x - 1]
                v2 = matrix[y][x]
                delta = (y + 1) * granularity - x * sampling
                previous = 0
                if x > 0 and (x - 1) * sampling >= y * granularity:
                    # x*g <= (y-1)*s <= y*s <= (x+1)*g <= (y+1)*s
                    #           |________|.......^
                    if x > 1:
                        previous = matrix[y][x - 2]
                    scale = sampling
                else:
                    # (y-1)*s < x*g <= y*s <= (x+1)*g <= (y+1)*s
                    #            |______|.......^
                    scale = sampling if x == 0 else x * sampling - y * granularity
                peak = v1 + (v1 - previous) / scale * delta
                if v2 > peak:
                    # we need to adjust the peak, it may not be less than the decayed value
                    if x < matrix.shape[1] - 1:
                        # y*s <= (x+1)*g <= (y+1)*s < (y+2)*s
                        #           ^.........|_________|
                        k = (v2 - matrix[y][x + 1]) / sampling  # > 0
                        peak = matrix[y][x] + k * ((x + 1) * sampling - (y + 1) * granularity)
                        # peak > v2 > v1
                    else:
                        peak = v2
                        # not enough data to interpolate; this is at least not restricted
                grow((y + 1) * granularity, peak)
                decay((y + 1) * granularity, peak)
            else:
                # (x+1)*granularity < y*sampling
                # y*sampling..(y+1)sampling
                decay(x * sampling, matrix[y][x - 1])
    return daily


def import_pandas():
    import pandas
    try:
        from pandas.plotting import register_matplotlib_converters
        register_matplotlib_converters()
    except ImportError:
        pass
    return pandas


def floor_datetime(dt, duration):
    return datetime.fromtimestamp(dt.timestamp() - dt.timestamp() % duration)


def load_burndown(
    header,
    name,
    matrix,
    resample,
    report_survival=True,
    interpolation_progress=False
):
    pandas = import_pandas()

    start, last, sampling, granularity, tick = header
    assert sampling > 0
    assert granularity > 0
    start = floor_datetime(datetime.fromtimestamp(start), tick)
    last = datetime.fromtimestamp(last)
    if report_survival:
        kmf = fit_kaplan_meier(matrix)
        if kmf is not None:
            print_survival_function(kmf, sampling)
    finish = start + timedelta(seconds=matrix.shape[1] * sampling * tick)
    if resample not in ("no", "raw"):
        print("resampling to %s, please wait..." % resample)
        # Interpolate the day x day matrix.
        # Each day brings equal weight in the granularity.
        # Sampling's interpolation is linear.
        daily = interpolate_burndown_matrix(
            matrix=matrix,
            granularity=granularity,
            sampling=sampling,
            progress=interpolation_progress,
        )
        daily[(last - start).days:] = 0
        # Resample the bands
        aliases = {
            "year": "A",
            "month": "M"
        }
        resample = aliases.get(resample, resample)
        periods = 0
        date_granularity_sampling = [start]
        while date_granularity_sampling[-1] < finish:
            periods += 1
            date_granularity_sampling = pandas.date_range(
                start, periods=periods, freq=resample)
        if date_granularity_sampling[0] > finish:
            if resample == "A":
                print("too loose resampling - by year, trying by month")
                return load_burndown(header, name, matrix, "month", report_survival=False)
            else:
                raise ValueError("Too loose resampling: %s. Try finer." % resample)
        date_range_sampling = pandas.date_range(
            date_granularity_sampling[0],
            periods=(finish - date_granularity_sampling[0]).days,
            freq="1D")
        # Fill the new square matrix
        matrix = numpy.zeros(
            (len(date_granularity_sampling), len(date_range_sampling)),
            dtype=numpy.float32)
        for i, gdt in enumerate(date_granularity_sampling):
            istart = (date_granularity_sampling[i - 1] - start).days \
                if i > 0 else 0
            ifinish = (gdt - start).days

            for j, sdt in enumerate(date_range_sampling):
                if (sdt - start).days >= istart:
                    break
            matrix[i, j:] = \
                daily[istart:ifinish, (sdt - start).days:].sum(axis=0)
        # Hardcode some cases to improve labels' readability
        if resample in ("year", "A"):
            labels = [dt.year for dt in date_granularity_sampling]
        elif resample in ("month", "M"):
            labels = [dt.strftime("%Y %B") for dt in date_granularity_sampling]
        else:
            labels = [dt.date() for dt in date_granularity_sampling]
    else:
        labels = [
            "%s - %s" % ((start + timedelta(seconds=i * granularity * tick)).date(),
                         (
                         start + timedelta(seconds=(i + 1) * granularity * tick)).date())
            for i in range(matrix.shape[0])]
        if len(labels) > 18:
            warnings.warn("Too many labels - consider resampling.")
        resample = "M"  # fake resampling type is checked while plotting
        date_range_sampling = pandas.date_range(
            start + timedelta(seconds=sampling * tick), periods=matrix.shape[1],
            freq="%dD" % sampling)
    return name, matrix, date_range_sampling, labels, granularity, sampling, resample


def load_ownership(header, sequence, contents, max_people, order_by_time):
    pandas = import_pandas()

    start, last, sampling, _, tick = header
    start = datetime.fromtimestamp(start)
    start = floor_datetime(start, tick)
    last = datetime.fromtimestamp(last)
    people = []
    for name in sequence:
        people.append(contents[name].sum(axis=1))
    people = numpy.array(people)
    date_range_sampling = pandas.date_range(
        start + timedelta(seconds=sampling * tick), periods=people[0].shape[0],
        freq="%dD" % sampling)

    if people.shape[0] > max_people:
        chosen = numpy.argpartition(-numpy.sum(people, axis=1), max_people)
        others = people[chosen[max_people:]].sum(axis=0)
        people = people[chosen[:max_people + 1]]
        people[max_people] = others
        sequence = [sequence[i] for i in chosen[:max_people]] + ["others"]
        print("Warning: truncated people to the most owning %d" % max_people)

    if order_by_time:
        appearances = numpy.argmax(people > 0, axis=1)
        if people.shape[0] > max_people:
            appearances[-1] = people.shape[1]
    else:
        appearances = -people.sum(axis=1)
        if people.shape[0] > max_people:
            appearances[-1] = 0
    order = numpy.argsort(appearances)
    people = people[order]
    sequence = [sequence[i] for i in order]

    for i, name in enumerate(sequence):
        if len(name) > 40:
            sequence[i] = name[:37] + "..."
    return sequence, people, date_range_sampling, last


def load_overwrites_matrix(people, matrix, max_people, normalize=True):
    matrix = matrix.astype(float)
    if matrix.shape[0] > max_people:
        order = numpy.argsort(-matrix[:, 0])
        matrix = matrix[order[:max_people]][:, [0, 1] + list(2 + order[:max_people])]
        people = [people[i] for i in order[:max_people]]
        print("Warning: truncated people to most productive %d" % max_people)
    if normalize:
        zeros = matrix[:, 0] == 0
        matrix[zeros, :] = 1
        matrix /= matrix[:, 0][:, None]
        matrix[zeros, :] = 0
    matrix = -matrix[:, 1:]
    for i, name in enumerate(people):
        if len(name) > 40:
            people[i] = name[:37] + "..."
    return people, matrix


def import_pyplot(backend, style):
    import matplotlib
    if backend:
        matplotlib.use(backend)
    from matplotlib import pyplot
    pyplot.style.use(style)
    print("matplotlib: backend is", matplotlib.get_backend())
    return matplotlib, pyplot


def apply_plot_style(figure, axes, legend, background, font_size, axes_size):
    foreground = "black" if background == "white" else "white"
    if axes_size is None:
        axes_size = (16, 12)
    else:
        axes_size = tuple(float(p) for p in axes_size.split(","))
    figure.set_size_inches(*axes_size)
    for side in ("bottom", "top", "left", "right"):
        axes.spines[side].set_color(foreground)
    for axis in (axes.xaxis, axes.yaxis):
        axis.label.update(dict(fontsize=font_size, color=foreground))
    for axis in ("x", "y"):
        getattr(axes, axis + "axis").get_offset_text().set_size(font_size)
        axes.tick_params(axis=axis, colors=foreground, labelsize=font_size)
    try:
        axes.ticklabel_format(axis="y", style="sci", scilimits=(0, 3))
    except AttributeError:
        pass
    figure.patch.set_facecolor(background)
    axes.set_facecolor(background)
    if legend is not None:
        frame = legend.get_frame()
        for setter in (frame.set_facecolor, frame.set_edgecolor):
            setter(background)
        for text in legend.get_texts():
            text.set_color(foreground)


def get_plot_path(base, name):
    root, ext = os.path.splitext(base)
    if not ext:
        ext = ".png"
    output = os.path.join(root, name + ext)
    os.makedirs(os.path.dirname(output), exist_ok=True)
    return output


def deploy_plot(title, output, background, tight=True):
    import matplotlib.pyplot as pyplot

    if not output:
        pyplot.gcf().canvas.set_window_title(title)
        pyplot.show()
    else:
        if title:
            pyplot.title(title, color="black" if background == "white" else "white")
        if tight:
            try:
                pyplot.tight_layout()
            except:  # noqa: E722
                print("Warning: failed to set the tight layout")
        print("Writing plot to %s" % output)
        pyplot.savefig(output, transparent=True)
    pyplot.clf()


def default_json(x):
    if hasattr(x, "tolist"):
        return x.tolist()
    if hasattr(x, "isoformat"):
        return x.isoformat()
    return x


def parse_date(text, default):
    if not text:
        return default
    from dateutil.parser import parse
    return parse(text)


def plot_burndown(args, target, name, matrix, date_range_sampling, labels, granularity,
                  sampling, resample):
    if args.output and args.output.endswith(".json"):
        data = locals().copy()
        del data["args"]
        data["type"] = "burndown"
        if args.mode == "project" and target == "project":
            output = args.output
        else:
            if target == "project":
                name = "project"
            output = get_plot_path(args.output, name)
        with open(output, "w") as fout:
            json.dump(data, fout, sort_keys=True, default=default_json)
        return

    matplotlib, pyplot = import_pyplot(args.backend, args.style)

    pyplot.stackplot(date_range_sampling, matrix, labels=labels)
    if args.relative:
        for i in range(matrix.shape[1]):
            matrix[:, i] /= matrix[:, i].sum()
        pyplot.ylim(0, 1)
        legend_loc = 3
    else:
        legend_loc = 2
    legend = pyplot.legend(loc=legend_loc, fontsize=args.font_size)
    pyplot.ylabel("Lines of code")
    pyplot.xlabel("Time")
    apply_plot_style(pyplot.gcf(), pyplot.gca(), legend, args.background,
                     args.font_size, args.size)
    pyplot.xlim(parse_date(args.start_date, date_range_sampling[0]),
                parse_date(args.end_date, date_range_sampling[-1]))
    locator = pyplot.gca().xaxis.get_major_locator()
    # set the optimal xticks locator
    if "M" not in resample:
        pyplot.gca().xaxis.set_major_locator(matplotlib.dates.YearLocator())
    locs = pyplot.gca().get_xticks().tolist()
    if len(locs) >= 16:
        pyplot.gca().xaxis.set_major_locator(matplotlib.dates.YearLocator())
        locs = pyplot.gca().get_xticks().tolist()
        if len(locs) >= 16:
            pyplot.gca().xaxis.set_major_locator(locator)
    if locs[0] < pyplot.xlim()[0]:
        del locs[0]
    endindex = -1
    if len(locs) >= 2 and pyplot.xlim()[1] - locs[-1] > (locs[-1] - locs[-2]) / 2:
        locs.append(pyplot.xlim()[1])
        endindex = len(locs) - 1
    startindex = -1
    if len(locs) >= 2 and locs[0] - pyplot.xlim()[0] > (locs[1] - locs[0]) / 2:
        locs.append(pyplot.xlim()[0])
        startindex = len(locs) - 1
    pyplot.gca().set_xticks(locs)
    # hacking time!
    labels = pyplot.gca().get_xticklabels()
    if startindex >= 0:
        labels[startindex].set_text(date_range_sampling[0].date())
        labels[startindex].set_text = lambda _: None
        labels[startindex].set_rotation(30)
        labels[startindex].set_ha("right")
    if endindex >= 0:
        labels[endindex].set_text(date_range_sampling[-1].date())
        labels[endindex].set_text = lambda _: None
        labels[endindex].set_rotation(30)
        labels[endindex].set_ha("right")
    title = "%s %d x %d (granularity %d, sampling %d)" % \
        ((name,) + matrix.shape + (granularity, sampling))
    output = args.output
    if output:
        if args.mode == "project" and target == "project":
            output = args.output
        else:
            if target == "project":
                name = "project"
            output = get_plot_path(args.output, name)
    deploy_plot(title, output, args.background)


def plot_many_burndown(args, target, header, parts):
    if not args.output:
        print("Warning: output not set, showing %d plots." % len(parts))
    stdout = io.StringIO()
    for name, matrix in tqdm.tqdm(parts):
        with contextlib.redirect_stdout(stdout):
            plot_burndown(args, target, *load_burndown(header, name, matrix, args.resample))
    sys.stdout.write(stdout.getvalue())


def plot_overwrites_matrix(args, repo, people, matrix):
    if args.output and args.output.endswith(".json"):
        data = locals().copy()
        del data["args"]
        data["type"] = "overwrites_matrix"
        if args.mode == "all":
            output = get_plot_path(args.output, "matrix")
        else:
            output = args.output
        with open(output, "w") as fout:
            json.dump(data, fout, sort_keys=True, default=default_json)
        return

    matplotlib, pyplot = import_pyplot(args.backend, args.style)

    s = 4 + matrix.shape[1] * 0.3
    fig = pyplot.figure(figsize=(s, s))
    ax = fig.add_subplot(111)
    ax.xaxis.set_label_position("top")
    ax.matshow(matrix, cmap=pyplot.cm.OrRd)
    ax.set_xticks(numpy.arange(0, matrix.shape[1]))
    ax.set_yticks(numpy.arange(0, matrix.shape[0]))
    ax.set_yticklabels(people, va="center")
    ax.set_xticks(numpy.arange(0.5, matrix.shape[1] + 0.5), minor=True)
    ax.set_xticklabels(["Unidentified"] + people, rotation=45, ha="left",
                       va="bottom", rotation_mode="anchor")
    ax.set_yticks(numpy.arange(0.5, matrix.shape[0] + 0.5), minor=True)
    ax.grid(False)
    ax.grid(which="minor")
    apply_plot_style(fig, ax, None, args.background, args.font_size, args.size)
    if not args.output:
        pos1 = ax.get_position()
        pos2 = (pos1.x0 + 0.15, pos1.y0 - 0.1, pos1.width * 0.9, pos1.height * 0.9)
        ax.set_position(pos2)
    if args.mode == "all" and args.output:
        output = get_plot_path(args.output, "matrix")
    else:
        output = args.output
    title = "%s %d developers overwrite" % (repo, matrix.shape[0])
    if args.output:
        # FIXME(vmarkovtsev): otherwise the title is screwed in savefig()
        title = ""
    deploy_plot(title, output, args.background)


def plot_ownership(args, repo, names, people, date_range, last):
    if args.output and args.output.endswith(".json"):
        data = locals().copy()
        del data["args"]
        data["type"] = "ownership"
        if args.mode == "all" and args.output:
            output = get_plot_path(args.output, "people")
        else:
            output = args.output
        with open(output, "w") as fout:
            json.dump(data, fout, sort_keys=True, default=default_json)
        return

    matplotlib, pyplot = import_pyplot(args.backend, args.style)

    polys = pyplot.stackplot(date_range, people, labels=names)
    if names[-1] == "others":
        polys[-1].set_hatch("/")
    pyplot.xlim(parse_date(args.start_date, date_range[0]), parse_date(args.end_date, last))

    if args.relative:
        for i in range(people.shape[1]):
            people[:, i] /= people[:, i].sum()
        pyplot.ylim(0, 1)
        legend_loc = 3
    else:
        legend_loc = 2
    ncol = 1 if len(names) < 15 else 2
    legend = pyplot.legend(loc=legend_loc, fontsize=args.font_size, ncol=ncol)
    apply_plot_style(pyplot.gcf(), pyplot.gca(), legend, args.background,
                     args.font_size, args.size)
    if args.mode == "all" and args.output:
        output = get_plot_path(args.output, "people")
    else:
        output = args.output
    deploy_plot("%s code ownership through time" % repo, output, args.background)


IDEAL_SHARD_SIZE = 4096


def train_embeddings(index, matrix, tmpdir, shard_size=IDEAL_SHARD_SIZE):
    import tensorflow as tf
    try:
        from . import swivel
    except (SystemError, ImportError):
        import swivel

    assert matrix.shape[0] == matrix.shape[1]
    assert len(index) <= matrix.shape[0]
    outlier_threshold = numpy.percentile(matrix.data, 99)
    matrix.data[matrix.data > outlier_threshold] = outlier_threshold
    nshards = len(index) // shard_size
    if nshards * shard_size < len(index):
        nshards += 1
        shard_size = len(index) // nshards
        nshards = len(index) // shard_size
    remainder = len(index) - nshards * shard_size
    if remainder > 0:
        lengths = matrix.indptr[1:] - matrix.indptr[:-1]
        filtered = sorted(numpy.argsort(lengths)[remainder:])
    else:
        filtered = list(range(len(index)))
    if len(filtered) < matrix.shape[0]:
        print("Truncating the sparse matrix...")
        matrix = matrix[filtered, :][:, filtered]
    meta_index = []
    for i, j in enumerate(filtered):
        meta_index.append((index[j], matrix[i, i]))
    index = [mi[0] for mi in meta_index]
    with tempfile.TemporaryDirectory(prefix="hercules_labours_", dir=tmpdir or None) as tmproot:
        print("Writing Swivel metadata...")
        vocabulary = "\n".join(index)
        with open(os.path.join(tmproot, "row_vocab.txt"), "w") as out:
            out.write(vocabulary)
        with open(os.path.join(tmproot, "col_vocab.txt"), "w") as out:
            out.write(vocabulary)
        del vocabulary
        bool_sums = matrix.indptr[1:] - matrix.indptr[:-1]
        bool_sums_str = "\n".join(map(str, bool_sums.tolist()))
        with open(os.path.join(tmproot, "row_sums.txt"), "w") as out:
            out.write(bool_sums_str)
        with open(os.path.join(tmproot, "col_sums.txt"), "w") as out:
            out.write(bool_sums_str)
        del bool_sums_str
        reorder = numpy.argsort(-bool_sums)

        print("Writing Swivel shards...")
        for row in range(nshards):
            for col in range(nshards):
                def _int64s(xs):
                    return tf.train.Feature(
                        int64_list=tf.train.Int64List(value=list(xs)))

                def _floats(xs):
                    return tf.train.Feature(
                        float_list=tf.train.FloatList(value=list(xs)))

                indices_row = reorder[row::nshards]
                indices_col = reorder[col::nshards]
                shard = matrix[indices_row][:, indices_col].tocoo()

                example = tf.train.Example(features=tf.train.Features(feature={
                    "global_row": _int64s(indices_row),
                    "global_col": _int64s(indices_col),
                    "sparse_local_row": _int64s(shard.row),
                    "sparse_local_col": _int64s(shard.col),
                    "sparse_value": _floats(shard.data)}))

                with open(os.path.join(tmproot, "shard-%03d-%03d.pb" % (row, col)), "wb") as out:
                    out.write(example.SerializeToString())
        print("Training Swivel model...")
        swivel.FLAGS.submatrix_rows = shard_size
        swivel.FLAGS.submatrix_cols = shard_size
        if len(meta_index) <= IDEAL_SHARD_SIZE / 16:
            embedding_size = 50
            num_epochs = 100000
        elif len(meta_index) <= IDEAL_SHARD_SIZE:
            embedding_size = 50
            num_epochs = 50000
        elif len(meta_index) <= IDEAL_SHARD_SIZE * 2:
            embedding_size = 60
            num_epochs = 10000
        elif len(meta_index) <= IDEAL_SHARD_SIZE * 4:
            embedding_size = 70
            num_epochs = 8000
        elif len(meta_index) <= IDEAL_SHARD_SIZE * 10:
            embedding_size = 80
            num_epochs = 5000
        elif len(meta_index) <= IDEAL_SHARD_SIZE * 25:
            embedding_size = 100
            num_epochs = 1000
        elif len(meta_index) <= IDEAL_SHARD_SIZE * 100:
            embedding_size = 200
            num_epochs = 600
        else:
            embedding_size = 300
            num_epochs = 300
        if os.getenv("CI"):
            # Travis, AppVeyor etc. during the integration tests
            num_epochs /= 10
        swivel.FLAGS.embedding_size = embedding_size
        swivel.FLAGS.input_base_path = tmproot
        swivel.FLAGS.output_base_path = tmproot
        swivel.FLAGS.loss_multiplier = 1.0 / shard_size
        swivel.FLAGS.num_epochs = num_epochs
        # Tensorflow 1.5 parses sys.argv unconditionally *applause*
        argv_backup = sys.argv[1:]
        del sys.argv[1:]
        swivel.main(None)
        sys.argv.extend(argv_backup)
        print("Reading Swivel embeddings...")
        embeddings = []
        with open(os.path.join(tmproot, "row_embedding.tsv")) as frow:
            with open(os.path.join(tmproot, "col_embedding.tsv")) as fcol:
                for i, (lrow, lcol) in enumerate(zip(frow, fcol)):
                    prow, pcol = (l.split("\t", 1) for l in (lrow, lcol))
                    assert prow[0] == pcol[0]
                    erow, ecol = \
                        (numpy.fromstring(p[1], dtype=numpy.float32, sep="\t")
                         for p in (prow, pcol))
                    embeddings.append((erow + ecol) / 2)
    return meta_index, embeddings


class CORSWebServer(object):
    def __init__(self):
        self.thread = threading.Thread(target=self.serve)
        self.server = None

    def serve(self):
        outer = self

        try:
            from http.server import HTTPServer, SimpleHTTPRequestHandler, test
        except ImportError:  # Python 2
            from BaseHTTPServer import HTTPServer, test
            from SimpleHTTPServer import SimpleHTTPRequestHandler

        class ClojureServer(HTTPServer):
            def __init__(self, *args, **kwargs):
                HTTPServer.__init__(self, *args, **kwargs)
                outer.server = self

        class CORSRequestHandler(SimpleHTTPRequestHandler):
            def end_headers(self):
                self.send_header("Access-Control-Allow-Origin", "*")
                SimpleHTTPRequestHandler.end_headers(self)

        test(CORSRequestHandler, ClojureServer)

    def start(self):
        self.thread.start()

    def stop(self):
        if self.running:
            self.server.shutdown()
            self.thread.join()

    @property
    def running(self):
        return self.server is not None


web_server = CORSWebServer()


def write_embeddings(name, output, run_server, index, embeddings):
    print("Writing Tensorflow Projector files...")
    if not output:
        output = "couples"
    if output.endswith(".json"):
        output = os.path.join(output[:-5], "couples")
        run_server = False
    metaf = "%s_%s_meta.tsv" % (output, name)
    with open(metaf, "w") as fout:
        fout.write("name\tcommits\n")
        for pair in index:
            fout.write("%s\t%s\n" % pair)
    print("Wrote", metaf)
    dataf = "%s_%s_data.tsv" % (output, name)
    with open(dataf, "w") as fout:
        for vec in embeddings:
            fout.write("\t".join(str(v) for v in vec))
            fout.write("\n")
    print("Wrote", dataf)
    jsonf = "%s_%s.json" % (output, name)
    with open(jsonf, "w") as fout:
        fout.write("""{
  "embeddings": [
    {
      "tensorName": "%s %s coupling",
      "tensorShape": [%s, %s],
      "tensorPath": "http://0.0.0.0:8000/%s",
      "metadataPath": "http://0.0.0.0:8000/%s"
    }
  ]
}
""" % (output, name, len(embeddings), len(embeddings[0]), dataf, metaf))
    print("Wrote %s" % jsonf)
    if run_server and not web_server.running:
        web_server.start()
    url = "http://projector.tensorflow.org/?config=http://0.0.0.0:8000/" + jsonf
    print(url)
    if run_server:
        if shutil.which("xdg-open") is not None:
            os.system("xdg-open " + url)
        else:
            browser = os.getenv("BROWSER", "")
            if browser:
                os.system(browser + " " + url)
            else:
                print("\t" + url)


def show_shotness_stats(data):
    top = sorted(((r.counters[i], i) for i, r in enumerate(data)), reverse=True)
    for count, i in top:
        r = data[i]
        print("%8d  %s:%s [%s]" % (count, r.file, r.name, r.internal_role))


def show_sentiment_stats(args, name, resample, start_date, data):
    from scipy.signal import convolve, slepian

    matplotlib, pyplot = import_pyplot(args.backend, args.style)

    start_date = datetime.fromtimestamp(start_date)
    data = sorted(data.items())
    mood = numpy.zeros(data[-1][0] + 1, dtype=numpy.float32)
    timeline = numpy.array([start_date + timedelta(days=i) for i in range(mood.shape[0])])
    for d, val in data:
        mood[d] = (0.5 - val.Value) * 2
    resolution = 32
    window = slepian(len(timeline) // resolution, 0.5)
    window /= window.sum()
    mood_smooth = convolve(mood, window, "same")
    pos = mood_smooth.copy()
    pos[pos < 0] = 0
    neg = mood_smooth.copy()
    neg[neg >= 0] = 0
    resolution = 4
    window = numpy.ones(len(timeline) // resolution)
    window /= window.sum()
    avg = convolve(mood, window, "same")
    pyplot.fill_between(timeline, pos, color="#8DB843", label="Positive")
    pyplot.fill_between(timeline, neg, color="#E14C35", label="Negative")
    pyplot.plot(timeline, avg, color="grey", label="Average", linewidth=5)
    legend = pyplot.legend(loc=1, fontsize=args.font_size)
    pyplot.ylabel("Comment sentiment")
    pyplot.xlabel("Time")
    apply_plot_style(pyplot.gcf(), pyplot.gca(), legend, args.background,
                     args.font_size, args.size)
    pyplot.xlim(parse_date(args.start_date, timeline[0]), parse_date(args.end_date, timeline[-1]))
    locator = pyplot.gca().xaxis.get_major_locator()
    # set the optimal xticks locator
    if "M" not in resample:
        pyplot.gca().xaxis.set_major_locator(matplotlib.dates.YearLocator())
    locs = pyplot.gca().get_xticks().tolist()
    if len(locs) >= 16:
        pyplot.gca().xaxis.set_major_locator(matplotlib.dates.YearLocator())
        locs = pyplot.gca().get_xticks().tolist()
        if len(locs) >= 16:
            pyplot.gca().xaxis.set_major_locator(locator)
    if locs[0] < pyplot.xlim()[0]:
        del locs[0]
    endindex = -1
    if len(locs) >= 2 and pyplot.xlim()[1] - locs[-1] > (locs[-1] - locs[-2]) / 2:
        locs.append(pyplot.xlim()[1])
        endindex = len(locs) - 1
    startindex = -1
    if len(locs) >= 2 and locs[0] - pyplot.xlim()[0] > (locs[1] - locs[0]) / 2:
        locs.append(pyplot.xlim()[0])
        startindex = len(locs) - 1
    pyplot.gca().set_xticks(locs)
    # hacking time!
    labels = pyplot.gca().get_xticklabels()
    if startindex >= 0:
        labels[startindex].set_text(timeline[0].date())
        labels[startindex].set_text = lambda _: None
        labels[startindex].set_rotation(30)
        labels[startindex].set_ha("right")
    if endindex >= 0:
        labels[endindex].set_text(timeline[-1].date())
        labels[endindex].set_text = lambda _: None
        labels[endindex].set_rotation(30)
        labels[endindex].set_ha("right")
    overall_pos = sum(2 * (0.5 - d[1].Value) for d in data if d[1].Value < 0.5)
    overall_neg = sum(2 * (d[1].Value - 0.5) for d in data if d[1].Value > 0.5)
    title = "%s sentiment +%.1f -%.1f δ=%.1f" % (
        name, overall_pos, overall_neg, overall_pos - overall_neg)
    if args.mode == "all" and args.output:
        output = get_plot_path(args.output, "sentiment")
    else:
        output = args.output
    deploy_plot(title, output, args.background)


def show_devs(args, name, start_date, end_date, people, days, max_people=50):
    from scipy.signal import convolve, slepian

    if len(people) > max_people:
        print("Picking top %s developers by commit count" % max_people)
        # pick top N developers by commit count
        commits = defaultdict(int)
        for devs in days.values():
            for dev, stats in devs.items():
                commits[dev] += stats.Commits
        commits = sorted(((v, k) for k, v in commits.items()), reverse=True)
        chosen_people = {people[k] for _, k in commits[:max_people]}
    else:
        chosen_people = set(people)
    dists, devseries, devstats, route = order_commits(chosen_people, days, people)
    route_map = {v: i for i, v in enumerate(route)}
    # determine clusters
    clusters = hdbscan_cluster_routed_series(dists, route)
    keys = list(devseries.keys())
    route = [keys[node] for node in route]
    print("Plotting")
    # smooth time series
    start_date = datetime.fromtimestamp(start_date)
    start_date = datetime(start_date.year, start_date.month, start_date.day)
    end_date = datetime.fromtimestamp(end_date)
    end_date = datetime(end_date.year, end_date.month, end_date.day)
    size = (end_date - start_date).days + 1
    plot_x = [start_date + timedelta(days=i) for i in range(size)]
    resolution = 64
    window = slepian(size // resolution, 0.5)
    final = numpy.zeros((len(devseries), size), dtype=numpy.float32)
    for i, s in enumerate(devseries.values()):
        arr = numpy.array(s).transpose()
        full_history = numpy.zeros(size, dtype=numpy.float32)
        mask = arr[0] < size
        full_history[arr[0][mask]] = arr[1][mask]
        final[route_map[i]] = convolve(full_history, window, "same")

    matplotlib, pyplot = import_pyplot(args.backend, args.style)
    pyplot.rcParams["figure.figsize"] = (32, 16)
    pyplot.rcParams["font.size"] = args.font_size
    prop_cycle = pyplot.rcParams["axes.prop_cycle"]
    colors = prop_cycle.by_key()["color"]
    fig, axes = pyplot.subplots(final.shape[0], 1)
    backgrounds = ("#C4FFDB", "#FFD0CD") if args.background == "white" else ("#05401C", "#40110E")
    max_cluster = numpy.max(clusters)
    for ax, series, cluster, dev_i in zip(axes, final, clusters, route):
        if cluster >= 0:
            color = colors[cluster % len(colors)]
            i = 1
            while color == "#777777":
                color = colors[(max_cluster + i) % len(colors)]
                i += 1
        else:
            # outlier
            color = "#777777"
        ax.fill_between(plot_x, series, color=color)
        ax.set_axis_off()
        author = people[dev_i]
        ax.text(0.03, 0.5, author[:36] + (author[36:] and "..."),
                horizontalalignment="right", verticalalignment="center",
                transform=ax.transAxes, fontsize=args.font_size,
                color="black" if args.background == "white" else "white")
        ds = devstats[dev_i]
        stats = "%5d %8s %8s" % (ds[0], _format_number(ds[1] - ds[2]), _format_number(ds[3]))
        ax.text(0.97, 0.5, stats,
                horizontalalignment="left", verticalalignment="center",
                transform=ax.transAxes, fontsize=args.font_size, family="monospace",
                backgroundcolor=backgrounds[ds[1] <= ds[2]],
                color="black" if args.background == "white" else "white")
    axes[0].text(0.97, 1.75, " cmts    delta  changed",
                 horizontalalignment="left", verticalalignment="center",
                 transform=axes[0].transAxes, fontsize=args.font_size, family="monospace",
                 color="black" if args.background == "white" else "white")
    axes[-1].set_axis_on()
    target_num_labels = 12
    num_months = (end_date.year - start_date.year) * 12 + end_date.month - start_date.month
    interval = int(numpy.ceil(num_months / target_num_labels))
    if interval >= 8:
        interval = int(numpy.ceil(num_months / (12 * target_num_labels)))
        axes[-1].xaxis.set_major_locator(matplotlib.dates.YearLocator(base=max(1, interval // 12)))
        axes[-1].xaxis.set_major_formatter(matplotlib.dates.DateFormatter("%Y"))
    else:
        axes[-1].xaxis.set_major_locator(matplotlib.dates.MonthLocator(interval=interval))
        axes[-1].xaxis.set_major_formatter(matplotlib.dates.DateFormatter("%Y-%m"))
    for tick in axes[-1].xaxis.get_major_ticks():
        tick.label.set_fontsize(args.font_size)
    axes[-1].spines["left"].set_visible(False)
    axes[-1].spines["right"].set_visible(False)
    axes[-1].spines["top"].set_visible(False)
    axes[-1].get_yaxis().set_visible(False)
    axes[-1].set_facecolor((1.0,) * 3 + (0.0,))

    title = ("%s commits" % name) if not args.output else ""
    if args.mode == "all" and args.output:
        output = get_plot_path(args.output, "time_series")
    else:
        output = args.output
    deploy_plot(title, output, args.background)


def order_commits(chosen_people, days, people):
    from seriate import seriate
    try:
        from fastdtw import fastdtw
    except ImportError as e:
        print("Cannot import fastdtw: %s\nInstall it from https://github.com/slaypni/fastdtw" % e)
        sys.exit(1)
    # FIXME(vmarkovtsev): remove once https://github.com/slaypni/fastdtw/pull/28 is merged&released
    try:
        sys.modules["fastdtw.fastdtw"].__norm = lambda p: lambda a, b: numpy.linalg.norm(
            numpy.atleast_1d(a) - numpy.atleast_1d(b), p)
    except KeyError:
        # the native extension does not have this bug
        pass

    devseries = defaultdict(list)
    devstats = defaultdict(lambda: DevDay(0, 0, 0, 0, {}))
    for day, devs in sorted(days.items()):
        for dev, stats in devs.items():
            if people[dev] in chosen_people:
                devseries[dev].append((day, stats.Commits))
                devstats[dev] = devstats[dev].add(stats)
    print("Calculating the distance matrix")
    # max-normalize the time series using a sliding window
    series = list(devseries.values())
    for i, s in enumerate(series):
        arr = numpy.array(s).transpose().astype(numpy.float32)
        arr[1] /= arr[1].sum()
        series[i] = arr.transpose()
    # calculate the distance matrix using dynamic time warping
    dists = numpy.full((len(series),) * 2, -100500, dtype=numpy.float32)
    # TODO: what's the total for this progress bar?
    with tqdm.tqdm() as pb:
        for x, serx in enumerate(series):
            dists[x, x] = 0
            for y, sery in enumerate(series[x + 1:], start=x + 1):
                min_day = int(min(serx[0][0], sery[0][0]))
                max_day = int(max(serx[-1][0], sery[-1][0]))
                arrx = numpy.zeros(max_day - min_day + 1, dtype=numpy.float32)
                arry = numpy.zeros_like(arrx)
                arrx[serx[:, 0].astype(int) - min_day] = serx[:, 1]
                arry[sery[:, 0].astype(int) - min_day] = sery[:, 1]
                # L1 norm
                dist, _ = fastdtw(arrx, arry, radius=5, dist=1)
                dists[x, y] = dists[y, x] = dist
                pb.update()
    print("Ordering the series")
    route = seriate(dists)
    return dists, devseries, devstats, route


def hdbscan_cluster_routed_series(dists, route):
    try:
        from hdbscan import HDBSCAN
    except ImportError as e:
        print("Cannot import hdbscan: %s" % e)
        sys.exit(1)

    opt_dist_chain = numpy.cumsum(numpy.array(
        [0] + [dists[route[i], route[i + 1]] for i in range(len(route) - 1)]))
    clusters = HDBSCAN(min_cluster_size=2).fit_predict(opt_dist_chain[:, numpy.newaxis])
    return clusters


def show_devs_efforts(args, name, start_date, end_date, people, days, max_people):
    from scipy.signal import convolve, slepian

    start_date = datetime.fromtimestamp(start_date)
    start_date = datetime(start_date.year, start_date.month, start_date.day)
    end_date = datetime.fromtimestamp(end_date)
    end_date = datetime(end_date.year, end_date.month, end_date.day)

    efforts_by_dev = defaultdict(int)
    for day, devs in days.items():
        for dev, stats in devs.items():
            efforts_by_dev[dev] += stats.Added + stats.Removed + stats.Changed
    if len(efforts_by_dev) > max_people:
        chosen = {v for k, v in sorted(
            ((v, k) for k, v in efforts_by_dev.items()), reverse=True)[:max_people]}
        print("Warning: truncated people to the most active %d" % max_people)
    else:
        chosen = set(efforts_by_dev)
    chosen_efforts = sorted(((efforts_by_dev[k], k) for k in chosen), reverse=True)
    chosen_order = {k: i for i, (_, k) in enumerate(chosen_efforts)}

    efforts = numpy.zeros((len(chosen) + 1, (end_date - start_date).days + 1), dtype=numpy.float32)
    for day, devs in days.items():
        if day < efforts.shape[1]:
            for dev, stats in devs.items():
                dev = chosen_order.get(dev, len(chosen_order))
                efforts[dev][day] += stats.Added + stats.Removed + stats.Changed
    efforts_cum = numpy.cumsum(efforts, axis=1)
    window = slepian(10, 0.5)
    window /= window.sum()
    for e in (efforts, efforts_cum):
        for i in range(e.shape[0]):
            ending = e[i][-len(window) * 2:].copy()
            e[i] = convolve(e[i], window, "same")
            e[i][-len(ending):] = ending
    matplotlib, pyplot = import_pyplot(args.backend, args.style)
    plot_x = [start_date + timedelta(days=i) for i in range(efforts.shape[1])]

    people = [people[k] for _, k in chosen_efforts] + ["others"]
    for i, name in enumerate(people):
        if len(name) > 40:
            people[i] = name[:37] + "..."

    polys = pyplot.stackplot(plot_x, efforts_cum, labels=people)
    if len(polys) == max_people + 1:
        polys[-1].set_hatch("/")
    polys = pyplot.stackplot(plot_x, -efforts * efforts_cum.max() / efforts.max())
    if len(polys) == max_people + 1:
        polys[-1].set_hatch("/")
    yticks = []
    for tick in pyplot.gca().yaxis.iter_ticks():
        if tick[1] >= 0:
            yticks.append(tick[1])
    pyplot.gca().yaxis.set_ticks(yticks)
    legend = pyplot.legend(loc=2, ncol=2, fontsize=args.font_size)
    apply_plot_style(pyplot.gcf(), pyplot.gca(), legend, args.background,
                     args.font_size, args.size or "16,10")
    if args.mode == "all" and args.output:
        output = get_plot_path(args.output, "efforts")
    else:
        output = args.output
    deploy_plot("Efforts through time (changed lines of code)", output, args.background)


def show_old_vs_new(args, name, start_date, end_date, people, days):
    from scipy.signal import convolve, slepian

    start_date = datetime.fromtimestamp(start_date)
    start_date = datetime(start_date.year, start_date.month, start_date.day)
    end_date = datetime.fromtimestamp(end_date)
    end_date = datetime(end_date.year, end_date.month, end_date.day)
    new_lines = numpy.zeros((end_date - start_date).days + 2)
    old_lines = numpy.zeros_like(new_lines)
    for day, devs in days.items():
        for stats in devs.values():
            new_lines[day] += stats.Added
            old_lines[day] += stats.Removed + stats.Changed
    resolution = 32
    window = slepian(max(len(new_lines) // resolution, 1), 0.5)
    new_lines = convolve(new_lines, window, "same")
    old_lines = convolve(old_lines, window, "same")
    matplotlib, pyplot = import_pyplot(args.backend, args.style)
    plot_x = [start_date + timedelta(days=i) for i in range(len(new_lines))]
    pyplot.fill_between(plot_x, new_lines, color="#8DB843", label="Changed new lines")
    pyplot.fill_between(plot_x, old_lines, color="#E14C35", label="Changed existing lines")
    pyplot.legend(loc=2, fontsize=args.font_size)
    for tick in chain(pyplot.gca().xaxis.get_major_ticks(), pyplot.gca().yaxis.get_major_ticks()):
        tick.label.set_fontsize(args.font_size)
    if args.mode == "all" and args.output:
        output = get_plot_path(args.output, "old_vs_new")
    else:
        output = args.output
    deploy_plot("Additions vs changes", output, args.background)


def show_languages(args, name, start_date, end_date, people, days):
    devlangs = defaultdict(lambda: defaultdict(lambda: numpy.zeros(3, dtype=int)))
    for day, devs in days.items():
        for dev, stats in devs.items():
            for lang, vals in stats.Languages.items():
                devlangs[dev][lang] += vals
    devlangs = sorted(devlangs.items(), key=lambda p: -sum(x.sum() for x in p[1].values()))
    for dev, ls in devlangs:
        print()
        print("#", people[dev])
        ls = sorted(((vals.sum(), lang) for lang, vals in ls.items()), reverse=True)
        for vals, lang in ls:
            if lang:
                print("%s: %d" % (lang, vals))


class ParallelDevData:
    def __init__(self):
        self.commits_rank = -1
        self.commits = -1
        self.lines_rank = -1
        self.lines = -1
        self.ownership_rank = -1
        self.ownership = -1
        self.couples_index = -1
        self.couples_cluster = -1
        self.commit_coocc_index = -1
        self.commit_coocc_cluster = -1

    def __str__(self):
        return str(self.__dict__)

    def __repr__(self):
        return str(self)


def load_devs_parallel(ownership, couples, devs, max_people):
    from seriate import seriate
    try:
        from hdbscan import HDBSCAN
    except ImportError as e:
        print("Cannot import ortools: %s\nInstall it from "
              "https://developers.google.com/optimization/install/python/" % e)
        sys.exit(1)

    people, owned = ownership
    _, cmatrix = couples
    _, days = devs

    print("calculating - commits")
    commits = defaultdict(int)
    for day, devs in days.items():
        for dev, stats in devs.items():
            commits[people[dev]] += stats.Commits
    chosen = [k for v, k in sorted(((v, k) for k, v in commits.items()),
                                   reverse=True)[:max_people]]
    result = {k: ParallelDevData() for k in chosen}
    for k, v in result.items():
        v.commits_rank = chosen.index(k)
        v.commits = commits[k]

    print("calculating - lines")
    lines = defaultdict(int)
    for day, devs in days.items():
        for dev, stats in devs.items():
            lines[people[dev]] += stats.Added + stats.Removed + stats.Changed
    lines_index = {k: i for i, (_, k) in enumerate(sorted(
        ((v, k) for k, v in lines.items() if k in chosen), reverse=True))}
    for k, v in result.items():
        v.lines_rank = lines_index[k]
        v.lines = lines[k]

    print("calculating - ownership")
    owned_index = {k: i for i, (_, k) in enumerate(sorted(
        ((owned[k][-1].sum(), k) for k in chosen), reverse=True))}
    for k, v in result.items():
        v.ownership_rank = owned_index[k]
        v.ownership = owned[k][-1].sum()

    print("calculating - couples")
    embeddings = numpy.genfromtxt(fname="couples_people_data.tsv", delimiter="\t")[
        [people.index(k) for k in chosen]]
    embeddings /= numpy.linalg.norm(embeddings, axis=1)[:, None]
    cos = embeddings.dot(embeddings.T)
    cos[cos > 1] = 1  # tiny precision faults
    dists = numpy.arccos(cos)
    clusters = HDBSCAN(min_cluster_size=2, metric="precomputed").fit_predict(dists)
    for k, v in result.items():
        v.couples_cluster = clusters[chosen.index(k)]

    couples_order = seriate(dists)
    roll_options = []
    for i in range(len(couples_order)):
        loss = 0
        for k, v in result.items():
            loss += abs(
                v.ownership_rank - (couples_order.index(chosen.index(k)) + i) % len(chosen))
        roll_options.append(loss)
    best_roll = numpy.argmin(roll_options)
    couples_order = list(numpy.roll(couples_order, best_roll))
    for k, v in result.items():
        v.couples_index = couples_order.index(chosen.index(k))

    print("calculating - commit series")
    dists, devseries, _, orig_route = order_commits(chosen, days, people)
    keys = list(devseries.keys())
    route = [keys[node] for node in orig_route]
    for roll in range(len(route)):
        loss = 0
        for k, v in result.items():
            i = route.index(people.index(k))
            loss += abs(v.couples_index - ((i + roll) % len(route)))
        roll_options[roll] = loss
    best_roll = numpy.argmin(roll_options)
    route = list(numpy.roll(route, best_roll))
    orig_route = list(numpy.roll(orig_route, best_roll))
    clusters = hdbscan_cluster_routed_series(dists, orig_route)
    for k, v in result.items():
        v.commit_coocc_index = route.index(people.index(k))
        v.commit_coocc_cluster = clusters[v.commit_coocc_index]

    return result


def show_devs_parallel(args, name, start_date, end_date, devs):
    matplotlib, pyplot = import_pyplot(args.backend, args.style)
    from matplotlib.collections import LineCollection

    def solve_equations(x1, y1, x2, y2):
        xcube = (x1 - x2) ** 3
        a = 2 * (y2 - y1) / xcube
        b = 3 * (y1 - y2) * (x1 + x2) / xcube
        c = 6 * (y2 - y1) * x1 * x2 / xcube
        d = y1 - a * x1 ** 3 - b * x1 ** 2 - c * x1
        return a, b, c, d

    # biggest = {k: max(getattr(d, k) for d in devs.values())
    #            for k in ("commits", "lines", "ownership")}
    for k, dev in devs.items():
        points = numpy.array([
            (1, dev.commits_rank),
            (2, dev.lines_rank),
            (3, dev.ownership_rank),
            (4, dev.couples_index),
            (5, dev.commit_coocc_index)],
            dtype=float)
        points[:, 1] = points[:, 1] / len(devs)
        splines = []
        for i in range(len(points) - 1):
            a, b, c, d = solve_equations(*points[i], *points[i + 1])
            x = numpy.linspace(i + 1, i + 2, 100)
            smooth_points = numpy.array(
                [x, a * x ** 3 + b * x ** 2 + c * x + d]).T.reshape(-1, 1, 2)
            splines.append(smooth_points)
        points = numpy.concatenate(splines)
        segments = numpy.concatenate([points[:-1], points[1:]], axis=1)
        lc = LineCollection(segments)
        lc.set_array(numpy.linspace(0, 0.1, segments.shape[0]))
        pyplot.gca().add_collection(lc)

    pyplot.xlim(0, 6)
    pyplot.ylim(-0.1, 1.1)
    deploy_plot("Developers", args.output, args.background)


def _format_number(n):
    if n == 0:
        return "0"
    power = int(numpy.log10(abs(n)))
    if power >= 6:
        n = n / 1000000
        if n >= 10:
            n = str(int(n))
        else:
            n = "%.1f" % n
            if n.endswith("0"):
                n = n[:-2]
        suffix = "M"
    elif power >= 3:
        n = n / 1000
        if n >= 10:
            n = str(int(n))
        else:
            n = "%.1f" % n
            if n.endswith("0"):
                n = n[:-2]
        suffix = "K"
    else:
        n = str(n)
        suffix = ""
    return n + suffix


def main():
    args = parse_args()
    reader = read_input(args)
    header = reader.get_header()
    name = reader.get_name()

    burndown_warning = "Burndown stats were not collected. Re-run hercules with --burndown."
    burndown_files_warning = \
        "Burndown stats for files were not collected. Re-run hercules with " \
        "--burndown --burndown-files."
    burndown_people_warning = \
        "Burndown stats for people were not collected. Re-run hercules with " \
        "--burndown --burndown-people."
    couples_warning = "Coupling stats were not collected. Re-run hercules with --couples."
    shotness_warning = "Structural hotness stats were not collected. Re-run hercules with " \
                       "--shotness. Also check --languages - the output may be empty."
    sentiment_warning = "Sentiment stats were not collected. Re-run hercules with --sentiment."
    devs_warning = "Devs stats were not collected. Re-run hercules with --devs."

    def run_times():
        rt = reader.get_run_times()
        pandas = import_pandas()
        series = pandas.to_timedelta(pandas.Series(rt).sort_values(ascending=False), unit="s")
        df = pandas.concat([series, series / series.sum()], axis=1)
        df.columns = ["time", "ratio"]
        print(df)

    def project_burndown():
        try:
            full_header = header + reader.get_burndown_parameters()
        except KeyError:
            print("project: " + burndown_warning)
            return
        plot_burndown(args, "project",
                      *load_burndown(full_header, *reader.get_project_burndown(),
                                     resample=args.resample, interpolation_progress=True))

    def files_burndown():
        try:
            full_header = header + reader.get_burndown_parameters()
        except KeyError:
            print(burndown_warning)
            return
        try:
            plot_many_burndown(args, "file", full_header, reader.get_files_burndown())
        except KeyError:
            print("files: " + burndown_files_warning)

    def people_burndown():
        try:
            full_header = header + reader.get_burndown_parameters()
        except KeyError:
            print(burndown_warning)
            return
        try:
            plot_many_burndown(args, "person", full_header, reader.get_people_burndown())
        except KeyError:
            print("people: " + burndown_people_warning)

    def overwrites_matrix():
        try:

            plot_overwrites_matrix(args, name, *load_overwrites_matrix(
                *reader.get_people_interaction(), max_people=args.max_people))
            people, matrix = load_overwrites_matrix(
                *reader.get_people_interaction(), max_people=1000000, normalize=False)
            from scipy.sparse import csr_matrix
            matrix = matrix[:, 1:]
            matrix = numpy.triu(matrix) + numpy.tril(matrix).T
            matrix = matrix + matrix.T
            matrix = csr_matrix(matrix)
            try:
                write_embeddings("overwrites", args.output, not args.disable_projector,
                                 *train_embeddings(people, matrix, tmpdir=args.tmpdir))
            except AttributeError as e:
                print("Training the embeddings is not possible: %s: %s", type(e).__name__, e)
        except KeyError:
            print("overwrites_matrix: " + burndown_people_warning)

    def ownership_burndown():
        try:
            full_header = header + reader.get_burndown_parameters()
        except KeyError:
            print(burndown_warning)
            return
        try:
            plot_ownership(args, name, *load_ownership(
                full_header, *reader.get_ownership_burndown(), max_people=args.max_people,
                order_by_time=args.order_ownership_by_time))
        except KeyError:
            print("ownership: " + burndown_people_warning)

    def couples_files():
        try:
            write_embeddings("files", args.output, not args.disable_projector,
                             *train_embeddings(*reader.get_files_coocc(),
                                               tmpdir=args.tmpdir))
        except KeyError:
            print(couples_warning)

    def couples_people():
        try:
            write_embeddings("people", args.output, not args.disable_projector,
                             *train_embeddings(*reader.get_people_coocc(),
                                               tmpdir=args.tmpdir))
        except KeyError:
            print(couples_warning)

    def couples_shotness():
        try:
            write_embeddings("shotness", args.output, not args.disable_projector,
                             *train_embeddings(*reader.get_shotness_coocc(),
                                               tmpdir=args.tmpdir))
        except KeyError:
            print(shotness_warning)

    def shotness():
        try:
            data = reader.get_shotness()
        except KeyError:
            print(shotness_warning)
            return
        show_shotness_stats(data)

    def sentiment():
        try:
            data = reader.get_sentiment()
        except KeyError:
            print(sentiment_warning)
            return
        show_sentiment_stats(args, reader.get_name(), args.resample, reader.get_header()[0], data)

    def devs():
        try:
            data = reader.get_devs()
        except KeyError:
            print(devs_warning)
            return
        show_devs(args, reader.get_name(), *reader.get_header(), *data,
                  max_people=args.max_people)

    def devs_efforts():
        try:
            data = reader.get_devs()
        except KeyError:
            print(devs_warning)
            return
        show_devs_efforts(args, reader.get_name(), *reader.get_header(), *data,
                          max_people=args.max_people)

    def old_vs_new():
        try:
            data = reader.get_devs()
        except KeyError:
            print(devs_warning)
            return
        show_old_vs_new(args, reader.get_name(), *reader.get_header(), *data)

    def languages():
        try:
            data = reader.get_devs()
        except KeyError:
            print(devs_warning)
            return
        show_languages(args, reader.get_name(), *reader.get_header(), *data)

    def devs_parallel():
        try:
            ownership = reader.get_ownership_burndown()
        except KeyError:
            print(burndown_people_warning)
            return
        try:
            couples = reader.get_people_coocc()
        except KeyError:
            print(couples_warning)
            return
        try:
            devs = reader.get_devs()
        except KeyError:
            print(devs_warning)
            return
        show_devs_parallel(args, reader.get_name(), *reader.get_header(),
                           load_devs_parallel(ownership, couples, devs, args.max_people))

    modes = {
        "run-times": run_times,
        "burndown-project": project_burndown,
        "burndown-file": files_burndown,
        "burndown-person": people_burndown,
        "overwrites-matrix": overwrites_matrix,
        "ownership": ownership_burndown,
        "couples-files": couples_files,
        "couples-people": couples_people,
        "couples-shotness": couples_shotness,
        "shotness": shotness,
        "sentiment": sentiment,
        "devs": devs,
        "devs-efforts": devs_efforts,
        "old-vs-new": old_vs_new,
        "languages": languages,
        "devs-parallel": devs_parallel,
    }

    if "all" in args.modes:
        all_mode = True
        args.modes = [
            "burndown-project",
            "overwrites-matrix",
            "ownership",
            "couples-files",
            "couples-people",
            "couples-shotness",
            "shotness",
            "devs",
            "devs-efforts",
        ]
    else:
        all_mode = False

    for mode in args.modes:
        if mode not in modes:
            print("Unknown mode: %s" % mode)
            continue

        print("Running: %s" % mode)
        # `args.mode` is required for path determination in the mode functions
        args.mode = ("all" if all_mode else mode)
        try:
            modes[mode]()
        except ImportError as ie:
            print("A module required by the %s mode was not found: %s" % (mode, ie))
            if not all_mode:
                raise

    if web_server.running:
        secs = int(os.getenv("COUPLES_SERVER_TIME", "60"))
        print("Sleeping for %d seconds, safe to Ctrl-C" % secs)
        sys.stdout.flush()
        try:
            time.sleep(secs)
        except KeyboardInterrupt:
            pass
        web_server.stop()


if __name__ == "__main__":
    sys.exit(main())