Merge branch 'pk'

overrides/partials/comments.html

@@ -0,0 +1,55 @@
+{% if page.meta.comments %}
+  <h2 id="__comments">{{ lang.t("meta.comments") }}</h2>
+  <!-- Insert generated snippet here -->
+  <script src="https://giscus.app/client.js"
+        data-repo="SpikingNeurons/toolcraft"
+        data-repo-id="MDEwOlJlcG9zaXRvcnk0MDQyMjM4Njc="
+        data-category="Announcements"
+        data-category-id="DIC_kwDOGBf3e84B_IOU"
+        data-mapping="pathname"
+        data-strict="0"
+        data-reactions-enabled="1"
+        data-emit-metadata="0"
+        data-input-position="bottom"
+        data-theme="preferred_color_scheme"
+        data-lang="en"
+        crossorigin="anonymous"
+        async>
+  </script>
+
+  <!-- Synchronize Giscus theme with palette -->
+  <script>
+    var giscus = document.querySelector("script[src*=giscus]")
+
+    // Set palette on initial load
+    var palette = __md_get("__palette")
+    if (palette && typeof palette.color === "object") {
+      var theme = palette.color.scheme === "slate"
+        ? "transparent_dark"
+        : "light"
+
+      // Instruct Giscus to set theme
+      giscus.setAttribute("data-theme", theme)
+    }
+
+    // Register event handlers after documented loaded
+    document.addEventListener("DOMContentLoaded", function() {
+      var ref = document.querySelector("[data-md-component=palette]")
+      ref.addEventListener("change", function() {
+        var palette = __md_get("__palette")
+        if (palette && typeof palette.color === "object") {
+          var theme = palette.color.scheme === "slate"
+            ? "transparent_dark"
+            : "light"
+
+          // Instruct Giscus to change theme
+          var frame = document.querySelector(".giscus-frame")
+          frame.contentWindow.postMessage(
+            { giscus: { setConfig: { theme } } },
+            "https://giscus.app"
+          )
+        }
+      })
+    })
+  </script>
+{% endif %}

toolcraft/error/validation.py

@@ -152,11 +152,11 @@ def __init__(self, *, value, to_be_value, msgs: MESSAGES_TYPE):
         ])
 
 
-class IsSliceOrListWithin(_CustomException):
+class IsIntOrSliceOrListWithin(_CustomException):
     def __init__(
         self,
         *,
-        value: t.Union[slice, t.List[int]],
+        value: t.Union[int, slice, t.List[int]],
         min_value: int,
         max_value: int,
         msgs: MESSAGES_TYPE,
@@ -206,6 +206,13 @@ def __init__(
                     ]
                     _raise = True
                     break
+        elif isinstance(value, int):
+            if not min_value <= value < max_value:
+                msgs += [
+                    f"The value {value} is not within range i.e. "
+                    f"between {min_value} and {max_value}",
+                ]
+                _raise = True
         else:
             msgs += [
                 f"Expected a int, slice or list of int instead found "

toolcraft/job/__base__.py

@@ -119,9 +119,19 @@ def delete(self):
                 ]
             )
 
-    def update(self, data: t.Dict[str, t.Any]):
-        # _LOGGER.info(msg=f"Updating tag {self.path}")
-        raise e.code.NotYetImplemented(msgs=[f"yet to implement {Tag.update}"])
+    def update(self, data: t.Dict[str, t.Any], allow_overwrite: bool = False, encoding: str = 'utf-8'):
+        _LOGGER.info(msg=f"Updating tag {self.path}")
+        _old_data = {}
+        if self.path.exists():
+            _old_data = self.path.read_yaml(encoding=encoding)
+        for _k in data.keys():
+            if _k in _old_data.keys():
+                if not allow_overwrite:
+                    raise e.validation.NotAllowed(
+                        msgs=[f"Cannot overwrite key {_k} in tag ..."]
+                    )
+        _old_data.update(data)
+        self.path.write_yaml(_old_data, encoding=encoding)
 
 
 @dataclasses.dataclass
@@ -450,23 +460,28 @@ class JobLaunchParameters:
     lsf_memory: int = None
 
     def __setattr__(self, key, value):
+        # test for lsf parameters
         if key.startswith("lsf_"):
             if not settings.IS_LSF:
                 raise e.code.CodingError(
                     msgs=["Do not try to set LSF launch parameters as this is not LSF environment."]
                 )
-        # noinspection PyUnresolvedReferences
+
+        # check if value is set multiple times
+        # noinspection PyUnresolvedReferences,DuplicatedCode
         _default_value = self.__class__.__dataclass_fields__[key].default
-        if _default_value == value:
-            raise e.code.CodingError(
-                msgs=[f"The launch parameter {key} cannot be set to default value {_default_value}"]
-            )
-        else:
-            if getattr(self, key) == value:
+        _current_value = getattr(self, key)
+        # this means incoming value is not default
+        if _default_value != value:
+            # this means that current value is already updated
+            if _current_value != _default_value:
                 raise e.code.CodingError(
-                    msgs=[f"The launch parameter {key} is already set to {value} and you cannot set it again"]
+                    msgs=[f"The launch parameter {key} is already set to non default value {_current_value}",
+                          f"You cannot update it again with new value {value}"]
                 )
-            super().__setattr__(key, value)
+
+        # set attr
+        super().__setattr__(key, value)
 
 
 @dataclasses.dataclass
@@ -490,9 +505,9 @@ def __setattr__(self, key, value):
         # ------------------------------------------- 01.01
         # check IS_ON_SINGLE_CPU
         if key == 'IS_ON_SINGLE_CPU':
-            if settings.IS_LSF:
+            if settings.IS_LSF and value:
                 raise e.code.CodingError(
-                    msgs=["You cannot set IS_ON_SINGLE_CPU on LSF platform"]
+                    msgs=["You cannot set IS_ON_SINGLE_CPU on LSF platform to True"]
                 )
         # ------------------------------------------- 01.02
         # check IS_LSF_JOB
@@ -613,6 +628,30 @@ def is_view_job(self) -> bool:
             else:
                 raise e.code.ShouldNeverHappen(msgs=[f"Check {sys.argv}"])
 
+    @property
+    def is_archive_job(self) -> bool:
+        if 'archive' in sys.argv:
+            if sys.argv[1] == 'archive':
+                return True
+            else:
+                raise e.code.ShouldNeverHappen(msgs=[f"Check {sys.argv}"])
+
+    @property
+    def is_unfinished_job(self) -> bool:
+        if 'unfinished' in sys.argv:
+            if sys.argv[1] == 'unfinished':
+                return True
+            else:
+                raise e.code.ShouldNeverHappen(msgs=[f"Check {sys.argv}"])
+
+    @property
+    def is_failed_job(self) -> bool:
+        if 'failed' in sys.argv:
+            if sys.argv[1] == 'failed':
+                return True
+            else:
+                raise e.code.ShouldNeverHappen(msgs=[f"Check {sys.argv}"])
+
     @property
     def is_launched(self) -> bool:
         return self.tag_manager.launched.exists()
@@ -791,10 +830,10 @@ def __init__(
                         "This is lsf environment and you are trying to run local job"
                     ]
                 )
-        elif self.is_view_job:
+        elif self.is_view_job or self.is_archive_job or self.is_unfinished_job or self.is_failed_job:
             ...
         else:
-            raise e.code.ShouldNeverHappen(msgs=[])
+            raise e.code.ShouldNeverHappen(msgs=[f"Check {sys.argv}"])
         # ------------------------------------------------------------------ 01.03
         # check single cpu
         if self.is_on_single_cpu:

toolcraft/job/cli.py

@@ -381,6 +381,7 @@ def archive(
         print("*"*30)
         print(_ps1_script_file.read_text())
         print("*"*30)
+        subprocess.run(["gedit", _ps1_script_file.as_posix()])
 
 
 @_APP.command(help="Copies from server to cwd.")

toolcraft/storage/file_group.py

@@ -310,17 +310,6 @@ def periodic_check_needed(self) -> bool:
     def is_outdated(self) -> bool:
         return False
 
-    # def __getattribute__(self, item: str) -> t.Any:
-    #     """
-    #     Helper method to access the files in group as annotated attributes.
-    #     """
-    #     # todo: if there is t.ClassVar annotation use their name to
-    #     #  resolve the file and get() it here ... so that we can get files in
-    #     #  FileGroup without file_key
-    #     # a way to detect if field is class var
-    #     # dataclasses._is_classvar('aa', typing)
-    #     ...
-
     def explore(self):
         # for open with select
         # subprocess.Popen(r'explorer /select,"sadasdfas"')
@@ -1231,14 +1220,10 @@ def dtype(self) -> t.Dict[str, t.Any]:
     @property
     @util.CacheResult
     def lengths(self) -> t.Dict[str, int]:
-        if self.is_created:
-            _shape = self.config.shape
-            return {
-                k: _shape[k][0] for k in self.file_keys
-            }
-        raise e.code.CodingError(
-            msgs=["You have not created files yet so you cannot use this property"]
-        )
+        _shape = self.shape
+        return {
+            k: _shape[k][0] for k in self.file_keys
+        }
 
     @property
     def has_arbitrary_lengths(self) -> bool:

toolcraft/texipy/__base__.py

@@ -813,7 +813,7 @@ def write(
         if make_pdf:
             from . import helper
             helper.make_pdf_with_pdflatex(
-                tex_file=_save_to_file,
+                main_tex_file=_save_to_file,
                 pdf_file=_save_to_file.parent /
                          (_save_to_file.name.split(".")[0] + ".pdf"),
                 clean=clean,

toolcraft/texipy/usepackage.sty

@@ -15,7 +15,7 @@
 \RequirePackage{subcaption} %
 \RequirePackage{ulem} %
 \RequirePackage{ragged2e} % https://www.overleaf.com/learn/latex/Text_alignment
-%\RequirePackage{todonotes}
+\RequirePackage{todonotes}
 
 % reguired for mathbb
 \RequirePackage{amsmath}

toolcraft/util.py

@@ -1215,18 +1215,28 @@ def io_is_dir_empty(_dir: pathlib.Path) -> bool:
     return _is_empty
 
 
-def find_free_port(localhost: bool):
+def find_open_port(start_port=49152, end_port=65535, raise_error: bool = True) -> t.Optional[int]:
     """
-    Inspired from
-    https://stackoverflow.com/questions/1365265/on-localhost-how-do-i-pick-a-free-port-number
+    Find an open port on the local machine between the specified range.
+    Returns the open port number or None if no port is found.
     """
-    with contextlib.closing(
-        socket.socket(socket.AF_INET, socket.SOCK_STREAM)
-    ) as _socket:
-        # use 'localhost' for local machines ... or else I assume that it will scan all network routes
-        _socket.bind(('localhost' if localhost else '', 0))
-        _socket.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
-        return _socket.getsockname()[1]
+    for _port in range(start_port, end_port):
+        try:
+            # Try to create a socket using TCP/IP
+            with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
+                # Try to bind to the port
+                s.bind(("", _port))
+                # If successful, return this port
+                return _port
+        except OSError:
+            # This will be raised if the port is already in use
+            pass
+    # No open port was found
+    if raise_error:
+        raise e.validation.NotAllowed(
+            msgs=["We did not find any open port"]
+        )
+    return None
 
 
 def npy_load(file: "s.Path", memmap: bool = False, shape=None, dtype=None, ) -> np.ndarray: