Finish refactoring, update generated documentation.

docs/container.md

@@ -9,20 +9,24 @@ implementation.
 Abstract Classes
 ----------------
 
-::: oarepo_c4gh.crypt4gh.aheader
+::: oarepo_c4gh.crypt4gh.common.header_packet
 
-::: oarepo_c4gh.crypt4gh.acrypt4gh
+::: oarepo_c4gh.crypt4gh.common.header
+
+::: oarepo_c4gh.crypt4gh.common.proto4gh
+
+::: oarepo_c4gh.crypt4gh.common.data_block
 
 Container Components
 --------------------
 
 ::: oarepo_c4gh.crypt4gh.crypt4gh
 
-::: oarepo_c4gh.crypt4gh.header
+::: oarepo_c4gh.crypt4gh.stream.stream4gh
 
-::: oarepo_c4gh.crypt4gh.header_packet
+::: oarepo_c4gh.crypt4gh.stream.header
 
-::: oarepo_c4gh.crypt4gh.data_block
+::: oarepo_c4gh.crypt4gh.stream.header_packet
 
 Data Keys
 ---------
@@ -43,4 +47,7 @@ Stream Writer
 
 ::: oarepo_c4gh.crypt4gh.writer
 
-::: oarepo_c4gh.crypt4gh.filter
+::: oarepo_c4gh.crypt4gh.filter.filter4gh
+
+::: oarepo_c4gh.crypt4gh.filter.header
+

oarepo_c4gh/crypt4gh/common/__init__.py

@@ -0,0 +1 @@
+"""Empty"""

oarepo_c4gh/crypt4gh/common/header_packet.py

@@ -1,6 +1,7 @@
 """Interface for packet headers.
 
 """
+
 from ...exceptions import Crypt4GHHeaderPacketException
 
 
@@ -29,7 +30,6 @@ def __init__(
         self._data_encryption_method = data_encryption_method
         self._data_encryption_key = data_encryption_key
 
-
     @property
     def is_data_encryption_parameters(self) -> bool:
         """A predicate for checking whether this packet contains DEK.

oarepo_c4gh/crypt4gh/filter/__init__.py

@@ -0,0 +1 @@
+"""Empty"""

oarepo_c4gh/crypt4gh/filter/header.py

@@ -1,6 +1,7 @@
 """This module implements filtered header on top of other Header
 implementation.
 """
+
 from ..common.header import Header
 from ...key.software import SoftwareKey
 import io
@@ -86,5 +87,3 @@ def magic_bytes(self) -> bytes:
     def version(self) -> int:
         """Returns the original version."""
         return self._original.version
-
-

oarepo_c4gh/crypt4gh/stream/__init__.py

@@ -0,0 +1 @@
+"""Empty"""

oarepo_c4gh/crypt4gh/stream/header_packet.py

@@ -1,19 +1,22 @@
 """Implementation of single Crypt4GH header packet parser.
 
 """
+
 from ..common.header_packet import HeaderPacket
 from ...key import KeyCollection
 import io
-from ..util import read_crypt4gh_stream_le_uint32, read_crypt4gh_bytes_le_uint32
+from ..util import (
+    read_crypt4gh_stream_le_uint32,
+    read_crypt4gh_bytes_le_uint32,
+)
 from nacl.bindings import crypto_aead_chacha20poly1305_ietf_decrypt
 from nacl.exceptions import CryptoError
 from ...exceptions import Crypt4GHHeaderPacketException
 
 
 class StreamHeaderPacket(HeaderPacket):
-    """Loads the header packet from stream.
+    """Loads the header packet from stream."""
 
-    """
     def __init__(
         self, reader_keys: KeyCollection, istream: io.RawIOBase
     ) -> None:

tests/test_key.py

@@ -25,6 +25,7 @@ def test_abstract_interface(self):
 
     def test_abstract_implementation(self):
         from oarepo_c4gh import Key
+
         class MyKey(Key):
             pass
 

tests/test_writer.py

@@ -21,6 +21,7 @@ class TestACrypt4GHHeader(unittest.TestCase):
     def test_abstract_packets(self):
         class MyHeader4GH(Header):
             pass
+
         MyHeader4GH.__abstractmethods__ = set()
         hdr = MyHeader4GH()
         assert hdr.packets is None, "Implementation in abstract class"
@@ -30,6 +31,7 @@ class MyHeader4GH(Header):
     def test_abstract_container(self):
         class MyCrypt4GH(Proto4GH):
             pass
+
         MyCrypt4GH.__abstractmethods__ = set()
         c4gh = MyCrypt4GH()
         assert c4gh.header is None, "Implementation in abstract class"