Remove deprecated functionalities

doc/apidoc.json

@@ -4,10 +4,6 @@
             "File",
             "TextFile"
         ],
-        "Temporary files" : [
-            "temp_dir",
-            "temp_file"
-        ],
         "Visualization utilities":[
             "set_font_size_in_coord",
             "AdaptiveFancyArrow"
@@ -260,16 +256,14 @@
             "superimpose",
             "superimpose_homologs",
             "superimpose_without_outliers",
-            "AffineTransformation",
-            "superimpose_apply"
+            "AffineTransformation"
         ],
         "Filters" : [
             "filter_canonical_nucleotides",
             "filter_nucleotides",
             "filter_canonical_amino_acids",
             "filter_amino_acids",
             "filter_carbohydrates",
-            "filter_backbone",
             "filter_peptide_backbone",
             "filter_phosphate_backbone",
             "filter_linear_bond_continuity",
@@ -281,17 +275,13 @@
             "filter_highest_occupancy_altloc"
         ],
         "Checks" : [
-            "check_id_continuity",
             "check_atom_id_continuity",
             "check_res_id_continuity",
             "check_backbone_continuity",
             "check_duplicate_atoms",
-            "check_bond_continuity",
             "check_linear_continuity"
         ],
         "Repair" : [
-            "renumber_atom_ids",
-            "renumber_res_ids",
             "create_continuous_res_ids",
             "infer_elements",
             "create_atom_names"

src/biotite/__init__.py

@@ -13,7 +13,6 @@
 __author__ = "Patrick Kunzmann"
 
 from .file import *
-from .temp import *
 from .copyable import *
 from .visualize import *
 from .version import __version__, __version_tuple__

src/biotite/application/viennarna/rnafold.py

@@ -65,7 +65,7 @@ def run(self):
             fasta_file.lines.append(self._constraints)
         fasta_file.write(self._in_file)
         self._in_file.flush()
-        
+
         options = [
             "--noPS",
             "-T", self._temperature,
@@ -87,11 +87,11 @@ def evaluate(self):
 
         self._free_energy = free_energy
         self._dotbracket = dotbracket
-    
+
     def clean_up(self):
         super().clean_up()
         cleanup_tempfile(self._in_file)
-    
+
     @requires_state(AppState.CREATED)
     def set_temperature(self, temperature):
         """
@@ -104,7 +104,7 @@ def set_temperature(self, temperature):
             The temperature.
         """
         self._temperature = str(temperature)
-    
+
     @requires_state(AppState.CREATED)
     def set_constraints(self, pairs=None, paired=None, unpaired=None,
                         downstream=None, upstream=None, enforce=False):
@@ -138,7 +138,7 @@ def set_constraints(self, pairs=None, paired=None, unpaired=None,
             pairs, paired, unpaired, downstream, upstream
         )
         self._enforce = enforce
-    
+
     @requires_state(AppState.JOINED)
     def get_free_energy(self):
         """
@@ -162,25 +162,6 @@ def get_free_energy(self):
         """
         return self._free_energy
 
-    @requires_state(AppState.JOINED)
-    def get_mfe(self):
-        """
-        Get the free energy (kcal/mol) of the suggested
-        secondary structure.
-
-        DEPRECATED: Use :meth:`get_free_energy()` instead.
-
-        Returns
-        -------
-        mfe : float
-            The minimum free energy.
-        """
-        warnings.warn(
-            "'get_mfe()' is deprecated, use 'get_free_energy()' instead",
-            DeprecationWarning
-        )
-        return self.get_free_energy()
-
     @requires_state(AppState.JOINED)
     def get_dot_bracket(self):
         """
@@ -243,7 +224,7 @@ def get_base_pairs(self):
     @staticmethod
     def compute_secondary_structure(sequence, bin_path="RNAfold"):
         """
-        Compute the minimum free energy secondary structure of a 
+        Compute the minimum free energy secondary structure of a
         ribonucleic acid sequence using *ViennaRNA's* *RNAfold* software.
 
         This is a convenience function, that wraps the

src/biotite/database/rcsb/download.py

@@ -15,11 +15,10 @@
 
 
 _standard_url = "https://files.rcsb.org/download/"
-_mmtf_url = "https://mmtf.rcsb.org/v1.0/full/"
 _bcif_url = "https://models.rcsb.org/"
 _fasta_url = "https://www.rcsb.org/fasta/entry/"
 
-_binary_formats = ["mmtf", "bcif"]
+_binary_formats = ["bcif"]
 
 
 def fetch(pdb_ids, format, target_path=None, overwrite=False, verbose=False):
@@ -34,7 +33,7 @@ def fetch(pdb_ids, format, target_path=None, overwrite=False, verbose=False):
     pdb_ids : str or iterable object of str
         A single PDB ID or a list of PDB IDs of the structure(s)
         to be downloaded.
-    format : {'pdb', 'pdbx', 'cif', 'mmcif', 'bcif', 'mmtf', 'fasta'}
+    format : {'pdb', 'pdbx', 'cif', 'mmcif', 'bcif', 'fasta'}
         The format of the files to be downloaded.
         ``'pdbx'``, ``'cif'`` and ``'mmcif'`` are synonyms for
         the same format.
@@ -120,10 +119,6 @@ def fetch(pdb_ids, format, target_path=None, overwrite=False, verbose=False):
                     r = requests.get(_bcif_url + id + ".bcif")
                     content = r.content
                     _assert_valid_file(r.text, id)
-                elif format == "mmtf":
-                    r = requests.get(_mmtf_url + id)
-                    content = r.content
-                    _assert_valid_file(r.text, id)
                 elif format == "fasta":
                     r = requests.get(_fasta_url + id)
                     content = r.text

src/biotite/file.py

@@ -27,13 +27,6 @@ class File(Copyable, metaclass=abc.ABCMeta):
     :func:`write()` method is used.
     """
 
-    def __init__(self):
-        # Support for deprecated instance method 'read()':
-        # When creating an instance, the 'read()' class method is
-        # replaced by the instance method, so that subsequent
-        # 'read()' calls are delegated to the instance method
-        self.read = self._deprecated_read
-
     @classmethod
     @abc.abstractmethod
     def read(cls, file):
@@ -54,23 +47,6 @@ def read(cls, file):
         """
         pass
 
-    def _deprecated_read(self, file, *args, **kwargs):
-        """
-        Support for deprecated instance method :func:`read()`.
-
-        Internally this calls the :func:`read()` class method and
-        replaces the data in `self` with the data from the newly created
-        :class:`File` object
-        """
-        warnings.warn(
-            "Instance method 'read()' is deprecated, "
-            "use class method instead",
-            DeprecationWarning
-        )
-        cls = type(self)
-        new_file = cls.read(file, *args, **kwargs)
-        self.__dict__.update(new_file.__dict__)
-
     @abc.abstractmethod
     def write(self, file):
         """

src/biotite/sequence/graphics/logo.py

@@ -48,12 +48,6 @@ def plot_sequence_logo(axes, profile, scheme=None, **kwargs):
 
     .. footbibliography::
     """
-    from matplotlib.text import Text
-
-    if isinstance(profile, Alignment):
-        warnings.warn("Using an alignment for this method is deprecated; use a profile instead", DeprecationWarning)
-        profile = SequenceProfile.from_alignment(profile)
-
     alphabet = profile.alphabet
     if not isinstance(alphabet, LetterAlphabet):
         raise TypeError("The sequences' alphabet must be a letter alphabet")