Standard library TODO

[inumanag]

Hi Jordan,

let's start with the string library:
https://docs.python.org/3/library/stdtypes.html#textseq

You can avoid string.format part for now.

Some functions (like str.split) are implemented in multiple places: for example, split on a single character is different than a split that operates on multi-character patterns.

Also, for each stdlib file, add the docs and implement a test suite as follows. For str.seq, add test_str.seq and there test each function, e.g.:

str.seq:

class str:
   def isspace(self: str) -> bool:
      """
      Doc
      """
      ...

test_str.seq:

def test_isspace():
    assert ' '.isspace() == True
    assert 'x'.isspace() == False
    # ... etc

Please check the function once done:

• str.capitalize()
• str.casefold()
• str.center(width[, fillchar])
• str.count(sub[, start[, end]])
• str.endswith(suffix[, start[, end]])
• str.expandtabs(tabsize=8)
• str.find(sub[, start[, end]])
• str.format(*args, **kwargs)
• str.index(sub[, start[, end]])
• str.isalnum()
• str.isalpha()
• str.isascii()
• str.isdecimal()
• str.isdigit()
• str.isidentifier()
• str.islower()
• str.isnumeric()
• str.isprintable()
• str.isspace()
• str.istitle()
• str.isupper()
• str.join(iterable)
• str.ljust(width[, fillchar])
• str.lower()
• str.lstrip([chars])
• str.partition(sep)
• str.replace(old, new[, count])
• str.rfind(sub[, start[, end]])
• str.rindex(sub[, start[, end]])
• str.rjust(width[, fillchar])
• str.rpartition(sep)
• str.rsplit(sep=None, maxsplit=-1)
• str.rstrip([chars])
• str.split(sep=None, maxsplit=-1)
• str.splitlines([keepends])
• str.startswith(prefix[, start[, end]])
• str.strip([chars])
• str.swapcase()
• str.title()
• str.translate(table)
• str.upper()
• str.zfill(width)

[inumanag]

Next step:
https://docs.python.org/3/library/math.html
https://docs.python.org/3/library/random.html
https://docs.python.org/3/library/statistics.html

[jordanwatson1]

Math

• math.ceil(x)
• math.copysign(x, y)
• math.fabs(x)
• math.factorial(x)
• math.floor(x)
• math.fmod(x, y)
• math.frexp(x)
• math.fsum(iterable)
• math.gcd(a, b)
• math.isclose(a, b, *, rel_tol=1e-09, abs_tol=0.0)
• math.isfinite(x)
• math.isinf(x)
• math.isnan(x)
• math.ldexp(x, i)
• math.modf(x)
• math.remainder(x, y)
• math.trunc(x)
• math.exp(x)
• math.expm1(x)
• math.log(x[, base])
• math.log1p(x)
• math.log2(x)
• math.log10(x)
• math.pow(x, y)
• math.sqrt(x)
• math.acos(x)
• math.asin(x)
• math.atan(x)
• math.atan2(y, x)
• math.cos(x)
• math.hypot(x, y)
• math.sin(x)
• math.tan(x)
• math.degrees(x)
• math.radians(x)
• math.acosh(x)
• math.asinh(x)
• math.atanh(x)
• math.cosh(x)
• math.sinh(x)
• math.tanh(x)
• math.erf(x)
• math.erfc(x)
• math.gamma(x)
• math.lgamma(x)
• math.pi
• math.e
• math.tau
• math.inf
• math.nan

[jordanwatson1]

Random

• random.seed(a=None, version=2)
• random.getstate()
• random.setstate(state)
• random.getrandbits(k)
• random.randrange(stop)
• random.randrange(start, stop[, step])
• random.randint(a, b)
• random.choice(seq)
• random.choices(population, weights=None, *, cum_weights=None, k=1)
• random.shuffle(x[, random])
• random.sample(population, k)
• random.random()
• random.uniform(a, b)
• random.triangular(low, high, mode)
• random.betavariate(alpha, beta)
• random.expovariate(lambd)
• random.gammavariate(alpha, beta)
• random.gauss(mu, sigma)
• random.lognormvariate(mu, sigma)
• random.normalvariate(mu, sigma)
• random.vonmisesvariate(mu, kappa)
• random.paretovariate(alpha)
• random.weibullvariate(alpha, beta)
• class random.Random([seed])
• class random.SystemRandom([seed])

[jordanwatson1]

itertools

• itertools.accumulate(iterable[, func, *, initial=None])
• itertools.chain(*iterables)
• classmethod chain.from_iterable(iterable)
• itertools.combinations(iterable, r)
• itertools.combinations_with_replacement(iterable, r)
• itertools.compress(data, selectors)
• itertools.count(start=0, step=1)
• itertools.cycle(iterable)
• itertools.dropwhile(predicate, iterable)
• itertools.filterfalse(predicate, iterable)
• itertools.groupby(iterable, key=None)
• itertools.islice(iterable, stop)
• itertools.islice(iterable, start, stop[, step])
• itertools.permutations(iterable, r=None)
• itertools.product(*iterables, repeat=1)
• itertools.repeat(object[, times])
• itertools.starmap(function, iterable)
• itertools.takewhile(predicate, iterable)
• itertools.tee(iterable, n=2)
• itertools.zip_longest(*iterables, fillvalue=None)

[inumanag]

Next steps:

• collections --- Counter, ChainMap, deque, defaultdict and OrderedDict
• bisect -- one part is already there
• heapq
• statistics
• os -- can you prepare the list of all os symbols that I can pick from later on?
• getopt

[jordanwatson1]

bisect

• bisect.bisect_left(a, x, lo=0, hi=len(a))
• bisect.bisect_right(a, x, lo=0, hi=len(a))
• bisect.bisect(a, x, lo=0, hi=len(a))
• bisect.insort_left(a, x, lo=0, hi=len(a))
• bisect.insort_right(a, x, lo=0, hi=len(a))
• bisect.insort(a, x, lo=0, hi=len(a))

[jordanwatson1]

collections

class collections.Counter([iterable-or-mapping])

• Counter.elements()
• Counter.most_common([n])
• Counter.subtract([iterable-or-mapping])
• Counter.fromkeys(iterable)
• Counter.update([iterable-or-mapping])

class collections.deque([iterable[, maxlen]])

• deque.append(x)
• deque.appendleft(x)
• deque.clear()
• deque.copy()
• deque.count(x)
• deque.extend(iterable)
• deque.extendleft(iterable)
• deque.index(x[, start[, stop]])
• deque.insert(i, x)
• deque.pop()
• deque.popleft()
• deque.remove(value)
• deque.reverse()
• deque.rotate(n=1)
• deque.maxlen

[jordanwatson1]

heapq

• heapq.heappush(heap, item)
• heapq.heappop(heap)
• heapq.heappushpop(heap, item)
• heapq.heapify(x)
• heapq.heapreplace(heap, item)
• heapq.merge(*iterables, key=None, reverse=False)
• heapq.nlargest(n, iterable, key=None)
• heapq.nsmallest(n, iterable, key=None)

[jordanwatson1]

statistics

• statistics.mean(data)
• statistics.fmean(data)
• statistics.geometric_mean(data)
• statistics.harmonic_mean(data)
• statistics.median(data)
• statistics.median_low(data)
• statistics.median_high(data)
• statistics.median_grouped(data, interval=1)
• statistics.mode(data)
• statistics.multimode(data)
• statistics.pstdev(data, mu=None)
• statistics.pvariance(data, mu=None)
• statistics.stdev(data, xbar=None)
• statistics.variance(data, xbar=None)
• statistics.quantiles(data, *, n=4, method='exclusive')
• class statistics.NormalDist(mu=0.0, sigma=1.0)
  • mean
  • median
  • mode
  • stdev
  • variance
  • classmethod from_samples(data)
  • samples(n, *, seed=None)
  • pdf(x)
  • cdf(x)
  • inv_cdf(p)
  • overlap(other)
  • quantiles(n=4)

[jordanwatson1]

os

• exception os.error
• os.name

Process Parameters

• os.ctermid()
• os.environ
• os.environb
• os.chdir(path)
• os.fchdir(fd)
• os.getcwd()
• os.fsencode(filename)
• os.fsdecode(filename)
• os.fspath(path)
• class os.PathLike
  • abstractmethod fspath()
• os.getenv(key, default=None)
• os.getenvb(key, default=None)
• os.get_exec_path(env=None)
• os.getegid()
• os.geteuid()
• os.getgid()
• os.getgrouplist(user, group)
• os.getgroups()
• os.getlogin()
• os.getpgid(pid)
• os.getpgrp()
• os.getpid()
• os.getppid()
• os.getpriority(which, who)
• os.PRIO_PROCESS
• os.PRIO_PGRP
• os.PRIO_USER
• os.getresuid()
• os.getresgid()
• os.getuid()
• os.initgroups(username, gid)
• os.putenv(key, value)
• os.setegid(egid)
• os.seteuid(euid)
• os.setgid(gid)
• os.setgroups(groups)
• os.setpgrp()
• os.setpgid(pid, pgrp)
• os.setpriority(which, who, priority)
• os.setregid(rgid, egid)
• os.setresgid(rgid, egid, sgid)
• os.setresuid(ruid, euid, suid)
• os.setreuid(ruid, euid)
• os.getsid(pid)
• os.setsid()
• os.setuid(uid)
• os.strerror(code)
• os.supports_bytes_environ
• os.umask(mask)
• os.uname()
• os.unsetenv(key)

File Object Creation

• os.fdopen(fd, *args, **kwargs)

File Descriptor Operations

• os.close(fd)
• os.closerange(fd_low, fd_high)
• os.copy_file_range(src, dst, count, offset_src=None, offset_dst=None)
• os.device_encoding(fd)
• os.dup(fd)
• os.dup2(fd, fd2, inheritable=True)
• os.fchmod(fd, mode)
• os.fchown(fd, uid, gid)
• os.fdatasync(fd)
• os.fpathconf(fd, name)
• os.fstat(fd)
• os.fstatvfs(fd)
• os.fsync(fd)
• os.ftruncate(fd, length)
• os.get_blocking(fd)
• os.isatty(fd)
• os.lockf(fd, cmd, len)
• os.F_LOCK
• os.F_TLOCK
• os.F_ULOCK
• os.F_TEST
• os.lseek(fd, pos, how)
• os.SEEK_SET
• os.SEEK_CUR
• os.SEEK_END
• os.open(path, flags, mode=0o777, *, dir_fd=None)
• os.O_RDONLY
• os.O_WRONLY
• os.O_RDWR
• os.O_APPEND
• os.O_CREAT
• os.O_EXCL
• os.O_TRUNC
• os.O_DSYNC
• os.O_RSYNC
• os.O_SYNC
• os.O_NDELAY
• os.O_NONBLOCK
• os.O_NOCTTY
• os.O_CLOEXEC
• os.O_BINARY
• os.O_NOINHERIT
• os.O_SHORT_LIVED
• os.O_TEMPORARY
• os.O_RANDOM
• os.O_SEQUENTIAL
• os.O_TEXT
• os.O_ASYNC
• os.O_DIRECT
• os.O_DIRECTORY
• os.O_NOFOLLOW
• os.O_NOATIME
• os.O_PATH
• os.O_TMPFILE
• os.O_SHLOCK
• os.O_EXLOCK
• os.openpty()
• os.pipe()
• os.pipe2(flags)
• os.posix_fallocate(fd, offset, len)
• os.posix_fadvise(fd, offset, len, advice)
• os.POSIX_FADV_NORMAL
• os.POSIX_FADV_SEQUENTIAL
• os.POSIX_FADV_RANDOM
• os.POSIX_FADV_NOREUSE
• os.POSIX_FADV_WILLNEED
• os.POSIX_FADV_DONTNEED
• os.pread(fd, n, offset)
• os.preadv(fd, buffers, offset, flags=0)
• os.RWF_NOWAIT
• os.RWF_HIPRI
• os.pwrite(fd, str, offset)
• os.pwritev(fd, buffers, offset, flags=0)
• os.RWF_DSYNC
• os.RWF_SYNC
• os.read(fd, n)
• os.sendfile(out, in, offset, count)
• os.sendfile(out, in, offset, count, [headers, ][trailers, ]flags=0)
• os.set_blocking(fd, blocking)
• os.SF_NODISKIO
• os.SF_MNOWAIT
• os.SF_SYNC
• os.readv(fd, buffers)
• os.tcgetpgrp(fd)
• os.tcsetpgrp(fd, pg)
• os.ttyname(fd)
• os.write(fd, str)
• os.writev(fd, buffers)

Querying the size of a terminal

• os.get_terminal_size(fd=STDOUT_FILENO)
• class os.terminal_size
  • columns
  • lines

Inheritance of File Descriptors

• os.get_inheritable(fd)
• os.set_inheritable(fd, inheritable)
• os.get_handle_inheritable(handle)
• os.set_handle_inheritable(handle, inheritable)

Files and Directories

• os.access(path, mode, *, dir_fd=None, effective_ids=False, follow_symlinks=True)
• os.F_OK
• os.R_OK
• os.W_OK
• os.X_OK
• os.chdir(path)
• os.chflags(path, flags, *, follow_symlinks=True)
• os.chmod(path, mode, *, dir_fd=None, follow_symlinks=True)
• os.chown(path, uid, gid, *, dir_fd=None, follow_symlinks=True)
• os.chroot(path)
• os.fchdir(fd)
• os.getcwd()
• os.getcwdb()
• os.lchflags(path, flags)
• os.lchmod(path, mode)
• os.lchown(path, uid, gid)
• os.link(src, dst, *, src_dir_fd=None, dst_dir_fd=None, follow_symlinks=True)
• os.listdir(path='.')
• os.lstat(path, *, dir_fd=None)
• os.mkdir(path, mode=0o777, *, dir_fd=None)
• os.makedirs(name, mode=0o777, exist_ok=False)
• os.mkfifo(path, mode=0o666, *, dir_fd=None)
• os.mknod(path, mode=0o600, device=0, *, dir_fd=None)
• os.major(device)
• os.minor(device)
• os.makedev(major, minor)
• os.pathconf(path, name)
• os.pathconf_names
• os.readlink(path, *, dir_fd=None)
• os.remove(path, *, dir_fd=None)
• os.removedirs(name)
• os.rename(src, dst, *, src_dir_fd=None, dst_dir_fd=None)
• os.renames(old, new)
• os.replace(src, dst, *, src_dir_fd=None, dst_dir_fd=None)
• os.rmdir(path, *, dir_fd=None)
• os.scandir(path='.')
• class os.DirEntry
  • name
  • path
  • inode()
  • is_dir(*, follow_symlinks=True)
  • is_file(*, follow_symlinks=True)
  • is_symlink()
  • stat(*, follow_symlinks=True)
• os.stat(path, *, dir_fd=None, follow_symlinks=True)
• class os.stat_result
  • st_mode
  • st_ino
  • st_dev
  • st_nlink
  • st_uid
  • st_gid
  • st_size
  • st_atime
  • st_mtime
  • st_ctime
  • st_atime_ns
  • st_mtime_ns
  • st_ctime_ns
  • st_blocks
  • st_blksize
  • st_rdev
  • st_flags
  • st_gen
  • st_birthtime
  • st_fstype
  • st_rsize
  • st_creator
  • st_type
  • st_file_attributes
  • st_reparse_tag
• os.statvfs(path)
• os.supports_dir_fd
• os.supports_effective_ids
• os.supports_fd
• os.supports_follow_symlinks
• os.symlink(src, dst, target_is_directory=False, *, dir_fd=None)
• os.sync()
• os.truncate(path, length)
• os.unlink(path, *, dir_fd=None)
• os.utime(path, times=None, *, [ns, ]dir_fd=None, follow_symlinks=True)
• os.walk(top, topdown=True, onerror=None, followlinks=False)
• os.fwalk(top='.', topdown=True, onerror=None, *, follow_symlinks=False, dir_fd=None)
• os.memfd_create(name[, flags=os.MFD_CLOEXEC])
• os.MFD_CLOEXEC
• os.MFD_ALLOW_SEALING
• os.MFD_HUGETLB
• os.MFD_HUGE_SHIFT
• os.MFD_HUGE_MASK
• os.MFD_HUGE_64KB
• os.MFD_HUGE_512KB
• os.MFD_HUGE_1MB
• os.MFD_HUGE_2MB
• os.MFD_HUGE_8MB
• os.MFD_HUGE_16MB
• os.MFD_HUGE_32MB
• os.MFD_HUGE_256MB
• os.MFD_HUGE_512MB
• os.MFD_HUGE_1GB
• os.MFD_HUGE_2GB
• os.MFD_HUGE_16GB

Linux extended attributes

• os.getxattr(path, attribute, *, follow_symlinks=True)
• os.listxattr(path=None, *, follow_symlinks=True)
• os.removexattr(path, attribute, *, follow_symlinks=True)
• os.setxattr(path, attribute, value, flags=0, *, follow_symlinks=True)
• os.XATTR_SIZE_MAX
• os.XATTR_CREATE
• os.XATTR_REPLACE

Process Management

• os.abort()
• os.add_dll_directory(path)
• os.execl(path, arg0, arg1, ...)
• os.execle(path, arg0, arg1, ..., env)
• os.execlp(file, arg0, arg1, ...)
• os.execlpe(file, arg0, arg1, ..., env)
• os.execv(path, args)
• os.execve(path, args, env)
• os.execvp(file, args)
• os.execvpe(file, args, env)
• os.EX_OK
• os.EX_USAGE
• os.EX_DATAERR
• os.EX_NOINPUT
• os.EX_NOUSER
• os.EX_NOHOST
• os.EX_UNAVAILABLE
• os.EX_SOFTWARE
• os.EX_OSERR
• os.EX_OSFILE
• os.EX_CANTCREAT
• os.EX_IOERR
• os.EX_TEMPFAIL
• os.EX_PROTOCOL
• os.EX_NOPERM
• os.EX_CONFIG
• os.EX_NOTFOUND
• os.fork()
• os.forkpty()
• os.kill(pid, sig)
• os.killpg(pgid, sig)
• os.nice(increment)
• os.plock(op)
• os.popen(cmd, mode='r', buffering=-1)
• os.posix_spawn(path, argv, env, *, file_actions=None, setpgroup=None, resetids=False, setsid=False, setsigmask=(), setsigdef=(), scheduler=None)
• os.posix_spawnp(path, argv, env, *, file_actions=None, setpgroup=None, resetids=False, setsid=False, setsigmask=(), setsigdef=(), scheduler=None)
• os.register_at_fork(*, before=None, after_in_parent=None, after_in_child=None)
• os.spawnl(mode, path, ...)
• os.spawnle(mode, path, ..., env)
• os.spawnlp(mode, file, ...)
• os.spawnlpe(mode, file, ..., env)
• os.spawnv(mode, path, args)
• os.spawnve(mode, path, args, env)
• os.spawnvp(mode, file, args)
• os.spawnvpe(mode, file, args, env)
• os.P_NOWAIT
• os.P_NOWAITO
• os.P_WAIT
• os.P_DETACH
• os.P_OVERLAY
• os.startfile(path[, operation])
• os.system(command)
• os.times()
• os.wait()
• os.waitid(idtype, id, options)
• os.P_PID
• os.P_PGID
• os.P_ALL
• os.WEXITED
• os.WSTOPPED
• os.WNOWAIT
• os.CLD_EXITED
• os.CLD_DUMPED
• os.CLD_TRAPPED
• os.CLD_CONTINUED
• os.waitpid(pid, options)
• os.wait3(options)
• os.wait4(pid, options)
• os.WNOHANG
• os.WCONTINUED
• os.WUNTRACED
• os.WCOREDUMP(status)
• os.WIFCONTINUED(status)
• os.WIFSTOPPED(status)
• os.WIFSIGNALED(status)
• os.WIFEXITED(status)
• os.WEXITSTATUS(status)
• os.WSTOPSIG(status)
• os.WTERMSIG(status)

Interface to the scheduler

• os.SCHED_OTHER
• os.SCHED_BATCH
• os.SCHED_IDLE
• os.SCHED_SPORADIC
• os.SCHED_FIFO
• os.SCHED_RR
• os.SCHED_RESET_ON_FORK
• class os.sched_param(sched_priority)
  • sched_priority
• os.sched_get_priority_min(policy)
• os.sched_get_priority_max(policy)
• os.sched_setscheduler(pid, policy, param)
• os.sched_getscheduler(pid)
• os.sched_setparam(pid, param)
• os.sched_getparam(pid)
• os.sched_rr_get_interval(pid)
• os.sched_yield()
• os.sched_setaffinity(pid, mask)
• os.sched_getaffinity(pid)

Miscellaneous System Information

• os.confstr(name)
• os.confstr_names
• os.cpu_count()
• os.getloadavg()
• os.sysconf(name)
• os.sysconf_names
• os.curdir
• os.pardir
• os.sep
• os.altsep
• os.extsep
• os.pathsep
• os.defpath
• os.linesep
• os.devnull
• os.RTLD_LAZY
• os.RTLD_NOW
• os.RTLD_GLOBAL
• os.RTLD_LOCAL
• os.RTLD_NODELETE
• os.RTLD_NOLOAD
• os.RTLD_DEEPBIND

Random numbers

• os.getrandom(size, flags=0)
• os.urandom(size)
• os.GRND_NONBLOCK
• os.GRND_RANDOM

[jordanwatson1]

getopt

• getopt.getopt(args, shortopts, longopts=[])
• getopt.gnu_getopt(args, shortopts, longopts=[])
• exception getopt.GetoptError
• exception getopt.error

[inumanag]

BioPython / pyVCF

Align

• Bio.Align.MultipleSeqAlignment
• Bio.Align.PairwiseAligner
• Bio.Align.PairwiseAlignment
• Bio.Align.PairwiseAlignments

SeqUtils

SeqRecord

SeqFeature

• Just a scaffolding

SearchIO

• BlatIO

pyVCF

SeqIO

• All base functions
• Submodules:
  • QualityIO
  • TabIO

GFF

Bio.kNN

Bio.triefind