aldepyde 0.0.0a1__py3-none-any.whl → 0.0.0a32__py3-none-any.whl

aldepyde/utils.py

@@ -0,0 +1,275 @@
+import sys
+import time
+
+# I'm sorry tqdm. I love you too :(
+# This is NOT meant to replace tqdm. Only bother using this if you are on
+# a restrictive system that doesn't allow 3rd party resources
+class ProgressBar():
+    def __init__(self, itb=None, ascii=False, blength=30, total=None, minupdate=.1, fp=sys.stdout):
+        self.itb = self.iterize(itb)
+        self.ascii = ascii
+        self.blength = blength
+        self.minupdate = minupdate
+        self._ascii_char = self.default_ascii()
+        self._uni_char = self.default_uni()
+        self._empty = self.default_empty()
+        self._progress_printer = self._print_bar if total != 0 else self._print_current
+        self.fp = fp
+        self.description = ""
+        self.current = 0
+        self.start = -1
+
+
+        if total is None:
+            try:
+                self.total = len(self.itb)
+            except TypeError:
+                self.total = 0
+        else:
+            self.total = total
+
+    def load(self, itb):
+        self.itb = self.iterize(itb)
+
+    def set_total(self, total):
+        self.total = total
+
+    def __iter__(self):
+        it = self.itb
+        minupdate = self.minupdate
+        self.start = last = time.perf_counter()
+        current = 0
+        pbar_type = self._print_current if self.total == 0 else self._print_bar
+        fp = self.fp
+        for item in iter(it):
+            yield item
+            current += 1
+            self.current = current
+            now = time.perf_counter()
+            if now - last >= minupdate:
+                last = now
+                fp.write("".join(["\r", self.description, pbar_type(current)]))
+        fp.write("".join(["\r", self.description , pbar_type(current)]))
+        fp.write('\n')
+
+    def update(self, current=1):
+        self.current += 1
+        if self.start == -1:
+            self.start = time.perf_counter()
+        if self.total == 0:
+            self.sp.write("".join(["\r", self.description ,self._print_current(self.current)]))
+        else:
+            self.fp.write("".join(["\r",self.description ,self._print_bar(self.current)]))
+
+    def _print_current(self, current:int) -> str:
+        return "".join([str(current), self._get_meta_current(current)])
+
+    def _get_meta_current(self, current):
+        elapsed = time.perf_counter() - self.start
+        eh, er = divmod(elapsed, 3600)
+        em, es = divmod(er, 60)
+        eh = int(eh)
+        em = int(em)
+        es = int(es)
+        rate = round(current / elapsed)
+        elp = "".join([str(eh).zfill(2), ':', str(em).zfill(2), ':', str(es).zfill(2)])
+        return "".join(['|', '|ELP ' , elp, '|', str(rate), ' itr/sec'])
+
+    def _print_bar(self, current:int) -> str:
+        completed = current / self.total
+        cycle = self._ascii_char if self.ascii else self._uni_char
+        if len(cycle) == 1:
+            return "".join([cycle[0]*round(completed*self.blength), self._empty*(self.blength - round(completed*self.blength)), self._get_meta_pbar(current)])
+        else:
+            full = min(len(cycle[-1] * int(completed * self.blength)), self.blength)
+            empty = self.blength - full - 1
+            bridge_index = round(((self.blength * completed)%1) * (len(cycle) - 1))
+            bridge = "" if empty < 0 else cycle[bridge_index]
+            return "".join( ['[', cycle[-1] * full, bridge, self._empty*empty, self._get_meta_pbar(current), ']'])
+
+
+    def _get_meta_pbar(self, current):
+        elapsed = time.perf_counter() - self.start
+        eh, er = divmod(elapsed, 3600)
+        em, es = divmod(er, 60)
+        eh = int(eh)
+        em = int(em)
+        es = int(es)
+        rate = round(current / elapsed)
+        eta = (self.total - current) / (rate + 0.00001)
+        h, r = divmod(eta, 3600)
+        m, s = divmod(r, 60)
+        h = int(h)
+        m = int(m)
+        s = int(s)
+        rs = "".join([str(h).zfill(2), ':', str(m).zfill(2), ':', str(s).zfill(2)])
+        elp = "".join([str(eh).zfill(2), ':', str(em).zfill(2), ':', str(es).zfill(2)])
+        return "".join(['|', str(round(100*current/self.total)), '%|ETA ', rs, '|ELP ' , elp, '|', str(rate), ' itr/sec'])
+
+
+    def iterize(self, itb):
+        if isinstance(itb, int):
+            return range(itb)
+        else:
+            try:
+                iter(itb)
+                return itb
+            except TypeError:
+                sys.stderr.write("The object loaded into the progress bar is not iterable")
+                return None
+
+    def default_empty(self):
+        return '-'
+
+    def set_empty(self, char: str):
+        if len(char) != 1:
+            raise ValueError("The empty character must only be one character")
+        self._empty = char
+
+    def default_ascii(self):
+        return ('@')
+
+    def set_ascii(self, progression : tuple):
+        self._ascii_char = progression
+
+    def default_uni(self):
+        return ('░', '▒', '▓', '█')
+
+    def set_uni(self, progression : tuple):
+        self._uni_char = progression
+
+    def set_description(self, desc):
+        self.description = desc
+
+
+
+
+class ProgressBar_dep():
+    def __init__(self, itb=None, force_ascii=False, force_spinner=False, bar_length=10):
+        self.itb = None
+        self.iterator = None
+        self.current = 0
+        self.total = 0
+        self.bar_length = bar_length
+        self.description = ""
+        self._force_ascii = force_ascii
+        self.empty = ' '
+        self.spinner = ['\\', '|', '/', '-']
+        # TODO Make _quarters adjustable
+        self._quarters = ['░', '▒', '▓', '█']
+        self.set_quarters(self._quarters)
+        self._force_spinner=force_spinner
+        self.set_force_ascii(self._force_ascii)
+        self.times = []
+        if itb is None:
+            return
+        else:
+            self.load(itb)
+
+    # Mostly for debugging
+    def set_force_spinner(self, force_spinner):
+        self._force_spinner = force_spinner
+
+    # Mostly for debugging
+    def set_force_ascii(self, force_ascii):
+        self._force_ascii = force_ascii
+        if not force_ascii:
+            self.spinner = ['⠋', '⠙', '⠹', '⠸', '⠼', '⠴', '⠦', '⠧', '⠇', '⠏']
+        else:
+            self.spinner = ['\\', '|', '/', '-']
+
+    def set_quarters(self, quarters):
+        self._quarters = [self.empty] + quarters
+
+    def set_total(self, total):
+        self.total = total
+
+    def load(self, itb):
+        if itb is not None:
+            if isinstance(itb, int):
+                itb = range(itb)
+            try:
+                iter(itb)
+                self.current = 0
+                self.description = ""
+                self.itb = itb
+                self.iterator = iter(self.itb)
+                try:
+                    self.total = len(itb)
+                except TypeError:
+                    self.total = 0
+
+            except TypeError:
+                print("The object loaded into the progress bar is not iterable", file=sys.stderr)
+
+
+    def update(self, updates : int):
+        self.current += updates
+
+    def set_description(self, description):
+        if description is None:
+            description = ""
+        self.description = description
+
+    # TODO Toggle ETA
+    def eta(self):
+        if len(self.times) == 2:
+            try:
+                seconds = (self.times[1] - self.times[0]) * (self.total - self.current)
+                hours, remainder = divmod(seconds, 3600)
+                minutes, sec = divmod(remainder, 60)
+                tstr = ""
+                if hours >= 1:
+                    tstr += f"{int(hours)}h "
+                if minutes >= 1:
+                    tstr += f"{int(minutes)}m "
+                tstr += f"{round(sec)}s "
+                return f" {{{tstr}}}"
+            except ZeroDivisionError:
+                return ""
+        else:
+            return ""
+
+    def push_time(self, t):
+        while len(self.times) >= 2:
+            self.times.pop(0)
+        self.times.append(t)
+
+    def _progress_as_bar(self) -> str:
+        return ""
+        try:
+            current_progress = self.current / self.total
+        except ZeroDivisionError:
+            return ""
+        if self._force_ascii:
+            current_progress = round(current_progress * self.bar_length)
+            return '*' * current_progress + '-' * (self.bar_length - current_progress)
+        else:
+            current_progress = current_progress * self.bar_length
+            whole_length = int(current_progress // 1)
+            whole_portion = self._quarters[-1] * whole_length
+            bp = round((current_progress%1) * 4)
+            bridge = self._quarters[bp]
+            decimal_portion = '-' * (self.bar_length - whole_length - 1)
+            return whole_portion + bridge + decimal_portion
+
+    def __iter__(self):
+        return self
+
+    def __next__(self):
+        try:
+            self.push_time(time())
+            item = next(self.iterator)
+
+            self.current += 1
+            d = " | " + self.description if len(self.description) != 0 else ""
+            return item
+
+            progress_statement = f"{self.current}/{self.total}" if self.total != 0 and not self._force_spinner else f"{self.current} {self.spinner[self.current % len(self.spinner)]}"
+            sys.stdout.write('\r' + self._progress_as_bar() + ' ' + progress_statement + d + self.eta())
+            sys.stdout.flush()
+            return item
+
+        except StopIteration:
+            print()
+            raise

{aldepyde-0.0.0a1.dist-info → aldepyde-0.0.0a32.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: aldepyde
-Version: 0.0.0a1
+Version: 0.0.0a32
 Summary: A package of chemistry and biochemical tools
 Author-email: Nate McMurray <nate.mcmurray13@gmail.com>
 License: MIT License
@@ -35,10 +35,11 @@ Classifier: Operating System :: OS Independent
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Dynamic: license-file
 
 <p align="left"><img src="https://github.com/cathepsin/aldepyde/blob/main/Aldepyde%20rough.png" height="250"/></p>
 
-#### A module for mangling biomolecules
+### A module for mangling biomolecules
 ---
 AldePYde is a module of spite. Being frustrated with either the lack of obscure potential or the difficult and steep learning curve of other similar modules,
 I made this. Here I present my various tools for chem/bioinformatics. This is all very much a work-in-progress, especially as I move over functionality from my

aldepyde-0.0.0a32.dist-info/RECORD

@@ -0,0 +1,43 @@
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+aldepyde/Parsers/_pdb_parser.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+aldepyde/biomolecule/Residue.py,sha256=CgTEIT7F4ljgxSscxzGU1AuThIRnX7i1mJ1DleUrcN0,172
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+aldepyde/rand/RandomProtein.py,sha256=CaFYJh8WiT5hvvWONXNkJAEVLefu7qPfnLi7WR5YL1g,16056
+aldepyde/rand/__init__.py,sha256=1EztGz5e6NRmKuAfp66trQDDa5ov-_ZkxrD9Zp8fScA,72
+aldepyde/stats/ProteinStats.py,sha256=t_gqhld2wKweszPZvtHhrORadFc28glFx5OgJs23TsM,2569
+aldepyde/stats/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+aldepyde-0.0.0a32.dist-info/licenses/LICENSE,sha256=VbOVaNlEaWa9cnYi8gOnenCBAVk9s_P3J_z-n_F-638,1091
+aldepyde-0.0.0a32.dist-info/METADATA,sha256=VpqfGzulHQ-omiPapAvVCVMIRGeTxPKUroF8FJkKBe8,2554
+aldepyde-0.0.0a32.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+aldepyde-0.0.0a32.dist-info/RECORD,,

{aldepyde-0.0.0a1.dist-info → aldepyde-0.0.0a32.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

aldepyde-0.0.0a32.dist-info/top_level.txt

@@ -0,0 +1 @@
+aldepyde

aldepyde-0.0.0a1.dist-info/RECORD

@@ -1,5 +0,0 @@
-aldepyde-0.0.0a1.dist-info/LICENSE,sha256=VbOVaNlEaWa9cnYi8gOnenCBAVk9s_P3J_z-n_F-638,1091
-aldepyde-0.0.0a1.dist-info/METADATA,sha256=grDlZURg0kPsDeLidwdcKOJdbhfgPSjEHj5PlzQtqhQ,2531
-aldepyde-0.0.0a1.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-aldepyde-0.0.0a1.dist-info/top_level.txt,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
-aldepyde-0.0.0a1.dist-info/RECORD,,

aldepyde-0.0.0a1.dist-info/top_level.txt

@@ -1 +0,0 @@
-