Update guide docs, remove outdated comments

docs/guide/extensions.ipynb

@@ -59,7 +59,7 @@
    "source": [
     "## STIX Extensions\n",
     "\n",
-    "This page is specific for the STIX Extensions mechanism defined in STIX 2.1 CS 02, for the deprecated STIX Customization mechanisms see the [Custom](custom.ipynb) section.\n",
+    "This page is specific for the STIX Extensions mechanism defined in STIX 2.1 CS 02. For the deprecated STIX Customization mechanisms see the [Custom](custom.ipynb) section.\n",
     "\n",
     "### Top Level Property Extensions\n",
     "\n",
@@ -336,7 +336,7 @@
    "source": [
     "### Using CustomExtension decorator\n",
     "\n",
-    "However, in order to prevent repetitive instantiation of the same extension, the `@CustomExtension` when used in a class for registering the `extension-definition` with stix2, it allows passing the id. Use the `extension_type` class variable to define what kind of extension it is."
+    "However, in order to prevent repetitive instantiation of the same extension, the `@CustomExtension` decorator can be used to register the `extension-definition` with stix2. Use the `extension_type` class variable to define what kind of extension it is. Then its id can be passed into objects that use this extension."
    ]
   },
   {
@@ -922,7 +922,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.9.2"
   }
  },
  "nbformat": 4,

docs/guide/markings.ipynb

@@ -77,8 +77,13 @@
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@@ -148,13 +153,13 @@
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@@ -265,8 +275,8 @@
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@@ -525,14 +545,19 @@
   },
   {
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    "outputs": [
     {
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@@ -602,15 +627,15 @@
        ".highlight .il { color: #666666 } /* Literal.Number.Integer.Long */</style><div class=\"highlight\"><pre><span></span><span class=\"p\">{</span>\n",
        "    <span class=\"nt\">&quot;type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;malware&quot;</span><span class=\"p\">,</span>\n",
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-       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:21:07.148194Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T13:59:56.556801Z&quot;</span><span class=\"p\">,</span>\n",
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        "    <span class=\"nt\">&quot;name&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;Poison Ivy&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;description&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;A ransomware related to ...&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;is_family&quot;</span><span class=\"p\">:</span> <span class=\"kc\">false</span><span class=\"p\">,</span>\n",
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        "        <span class=\"p\">{</span>\n",
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        "            <span class=\"nt\">&quot;selectors&quot;</span><span class=\"p\">:</span> <span class=\"p\">[</span>\n",
        "                <span class=\"s2\">&quot;description&quot;</span>\n",
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@@ -629,7 +654,7 @@
        "<IPython.core.display.HTML object>"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 7,
      "metadata": {},
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     }
@@ -662,7 +687,7 @@
   },
   {
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-   "execution_count": 9,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
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@@ -706,14 +731,19 @@
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   {
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+       "span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       ".highlight .hll { background-color: #ffffcc }\n",
+       ".highlight { background: #f8f8f8; }\n",
        ".highlight .c { color: #408080; font-style: italic } /* Comment */\n",
        ".highlight .err { border: 1px solid #FF0000 } /* Error */\n",
        ".highlight .k { color: #008000; font-weight: bold } /* Keyword */\n",
@@ -783,16 +813,16 @@
        ".highlight .il { color: #666666 } /* Literal.Number.Integer.Long */</style><div class=\"highlight\"><pre><span></span><span class=\"p\">{</span>\n",
        "    <span class=\"nt\">&quot;type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;spec_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--46498844-7689-4e7b-be25-b119d8401159&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--a315ce0b-1211-478e-812a-cd6d3eecc3c1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T20:55:56.088861Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T13:59:48.911595Z&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:21:39.898475Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:00:01.165749Z&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;[file:hashes.md5 = &#39;d41d8cd98f00b204e9800998ecf8427e&#39;]&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern_type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;stix&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T20:55:56.088861Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T13:59:48.911595Z&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;object_marking_refs&quot;</span><span class=\"p\">:</span> <span class=\"p\">[</span>\n",
-       "        <span class=\"s2\">&quot;marking-definition--f88d31f6-486f-44da-b317-01333bde0b82&quot;</span><span class=\"p\">,</span>\n",
+       "        <span class=\"s2\">&quot;marking-definition--4b8e86b5-d505-46a4-91b4-a8db17f4ff4d&quot;</span><span class=\"p\">,</span>\n",
-       "        <span class=\"s2\">&quot;marking-definition--9a4efc30-a7ac-42d0-8776-16f390a0fd44&quot;</span>\n",
+       "        <span class=\"s2\">&quot;marking-definition--f88d31f6-486f-44da-b317-01333bde0b82&quot;</span>\n",
        "    <span class=\"p\">]</span>\n",
        "<span class=\"p\">}</span>\n",
        "</pre></div>\n"
@@ -801,7 +831,7 @@
        "<IPython.core.display.HTML object>"
       ]
      },
-     "execution_count": 10,
+     "execution_count": 9,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -820,14 +850,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/html": [
-       "<style type=\"text/css\">.highlight .hll { background-color: #ffffcc }\n",
+       "<style type=\"text/css\">pre { line-height: 125%; }\n",
-       ".highlight  { background: #f8f8f8; }\n",
+       "td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       ".highlight .hll { background-color: #ffffcc }\n",
+       ".highlight { background: #f8f8f8; }\n",
        ".highlight .c { color: #408080; font-style: italic } /* Comment */\n",
        ".highlight .err { border: 1px solid #FF0000 } /* Error */\n",
        ".highlight .k { color: #008000; font-weight: bold } /* Keyword */\n",
@@ -897,13 +932,13 @@
        ".highlight .il { color: #666666 } /* Literal.Number.Integer.Long */</style><div class=\"highlight\"><pre><span></span><span class=\"p\">{</span>\n",
        "    <span class=\"nt\">&quot;type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;spec_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--46498844-7689-4e7b-be25-b119d8401159&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--a315ce0b-1211-478e-812a-cd6d3eecc3c1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T20:55:56.088861Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T13:59:48.911595Z&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:21:43.529702Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:00:03.00911Z&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;[file:hashes.md5 = &#39;d41d8cd98f00b204e9800998ecf8427e&#39;]&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern_type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;stix&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T20:55:56.088861Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T13:59:48.911595Z&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;object_marking_refs&quot;</span><span class=\"p\">:</span> <span class=\"p\">[</span>\n",
        "        <span class=\"s2\">&quot;marking-definition--f88d31f6-486f-44da-b317-01333bde0b82&quot;</span>\n",
        "    <span class=\"p\">]</span>\n",
@@ -914,21 +949,142 @@
        "<IPython.core.display.HTML object>"
       ]
      },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "indicator5 = indicator4.remove_markings(marking_definition)\n",
+    "print(indicator5.serialize(pretty=True))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The markings on an object can be replaced with a different set of markings:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<style type=\"text/css\">pre { line-height: 125%; }\n",
+       "td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       ".highlight .hll { background-color: #ffffcc }\n",
+       ".highlight { background: #f8f8f8; }\n",
+       ".highlight .c { color: #408080; font-style: italic } /* Comment */\n",
+       ".highlight .err { border: 1px solid #FF0000 } /* Error */\n",
+       ".highlight .k { color: #008000; font-weight: bold } /* Keyword */\n",
+       ".highlight .o { color: #666666 } /* Operator */\n",
+       ".highlight .ch { color: #408080; font-style: italic } /* Comment.Hashbang */\n",
+       ".highlight .cm { color: #408080; font-style: italic } /* Comment.Multiline */\n",
+       ".highlight .cp { color: #BC7A00 } /* Comment.Preproc */\n",
+       ".highlight .cpf { color: #408080; font-style: italic } /* Comment.PreprocFile */\n",
+       ".highlight .c1 { color: #408080; font-style: italic } /* Comment.Single */\n",
+       ".highlight .cs { color: #408080; font-style: italic } /* Comment.Special */\n",
+       ".highlight .gd { color: #A00000 } /* Generic.Deleted */\n",
+       ".highlight .ge { font-style: italic } /* Generic.Emph */\n",
+       ".highlight .gr { color: #FF0000 } /* Generic.Error */\n",
+       ".highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */\n",
+       ".highlight .gi { color: #00A000 } /* Generic.Inserted */\n",
+       ".highlight .go { color: #888888 } /* Generic.Output */\n",
+       ".highlight .gp { color: #000080; font-weight: bold } /* Generic.Prompt */\n",
+       ".highlight .gs { font-weight: bold } /* Generic.Strong */\n",
+       ".highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */\n",
+       ".highlight .gt { color: #0044DD } /* Generic.Traceback */\n",
+       ".highlight .kc { color: #008000; font-weight: bold } /* Keyword.Constant */\n",
+       ".highlight .kd { color: #008000; font-weight: bold } /* Keyword.Declaration */\n",
+       ".highlight .kn { color: #008000; font-weight: bold } /* Keyword.Namespace */\n",
+       ".highlight .kp { color: #008000 } /* Keyword.Pseudo */\n",
+       ".highlight .kr { color: #008000; font-weight: bold } /* Keyword.Reserved */\n",
+       ".highlight .kt { color: #B00040 } /* Keyword.Type */\n",
+       ".highlight .m { color: #666666 } /* Literal.Number */\n",
+       ".highlight .s { color: #BA2121 } /* Literal.String */\n",
+       ".highlight .na { color: #7D9029 } /* Name.Attribute */\n",
+       ".highlight .nb { color: #008000 } /* Name.Builtin */\n",
+       ".highlight .nc { color: #0000FF; font-weight: bold } /* Name.Class */\n",
+       ".highlight .no { color: #880000 } /* Name.Constant */\n",
+       ".highlight .nd { color: #AA22FF } /* Name.Decorator */\n",
+       ".highlight .ni { color: #999999; font-weight: bold } /* Name.Entity */\n",
+       ".highlight .ne { color: #D2413A; font-weight: bold } /* Name.Exception */\n",
+       ".highlight .nf { color: #0000FF } /* Name.Function */\n",
+       ".highlight .nl { color: #A0A000 } /* Name.Label */\n",
+       ".highlight .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */\n",
+       ".highlight .nt { color: #008000; font-weight: bold } /* Name.Tag */\n",
+       ".highlight .nv { color: #19177C } /* Name.Variable */\n",
+       ".highlight .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */\n",
+       ".highlight .w { color: #bbbbbb } /* Text.Whitespace */\n",
+       ".highlight .mb { color: #666666 } /* Literal.Number.Bin */\n",
+       ".highlight .mf { color: #666666 } /* Literal.Number.Float */\n",
+       ".highlight .mh { color: #666666 } /* Literal.Number.Hex */\n",
+       ".highlight .mi { color: #666666 } /* Literal.Number.Integer */\n",
+       ".highlight .mo { color: #666666 } /* Literal.Number.Oct */\n",
+       ".highlight .sa { color: #BA2121 } /* Literal.String.Affix */\n",
+       ".highlight .sb { color: #BA2121 } /* Literal.String.Backtick */\n",
+       ".highlight .sc { color: #BA2121 } /* Literal.String.Char */\n",
+       ".highlight .dl { color: #BA2121 } /* Literal.String.Delimiter */\n",
+       ".highlight .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */\n",
+       ".highlight .s2 { color: #BA2121 } /* Literal.String.Double */\n",
+       ".highlight .se { color: #BB6622; font-weight: bold } /* Literal.String.Escape */\n",
+       ".highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */\n",
+       ".highlight .si { color: #BB6688; font-weight: bold } /* Literal.String.Interpol */\n",
+       ".highlight .sx { color: #008000 } /* Literal.String.Other */\n",
+       ".highlight .sr { color: #BB6688 } /* Literal.String.Regex */\n",
+       ".highlight .s1 { color: #BA2121 } /* Literal.String.Single */\n",
+       ".highlight .ss { color: #19177C } /* Literal.String.Symbol */\n",
+       ".highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */\n",
+       ".highlight .fm { color: #0000FF } /* Name.Function.Magic */\n",
+       ".highlight .vc { color: #19177C } /* Name.Variable.Class */\n",
+       ".highlight .vg { color: #19177C } /* Name.Variable.Global */\n",
+       ".highlight .vi { color: #19177C } /* Name.Variable.Instance */\n",
+       ".highlight .vm { color: #19177C } /* Name.Variable.Magic */\n",
+       ".highlight .il { color: #666666 } /* Literal.Number.Integer.Long */</style><div class=\"highlight\"><pre><span></span><span class=\"p\">{</span>\n",
+       "    <span class=\"nt\">&quot;type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;spec_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--a315ce0b-1211-478e-812a-cd6d3eecc3c1&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T13:59:48.911595Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:00:04.531083Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;pattern&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;[file:hashes.md5 = &#39;d41d8cd98f00b204e9800998ecf8427e&#39;]&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;pattern_type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;stix&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;pattern_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T13:59:48.911595Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;object_marking_refs&quot;</span><span class=\"p\">:</span> <span class=\"p\">[</span>\n",
+       "        <span class=\"s2\">&quot;marking-definition--34098fce-860f-48ae-8e50-ebd3cc5e41da&quot;</span><span class=\"p\">,</span>\n",
+       "        <span class=\"s2\">&quot;marking-definition--4b8e86b5-d505-46a4-91b4-a8db17f4ff4d&quot;</span>\n",
+       "    <span class=\"p\">]</span>\n",
+       "<span class=\"p\">}</span>\n",
+       "</pre></div>\n"
+      ],
+      "text/plain": [
+       "<IPython.core.display.HTML object>"
+      ]
+     },
      "execution_count": 11,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "indicator5 = indicator4.remove_markings(marking_definition)\n",
+    "from stix2 import TLP_GREEN\n",
-    "print(indicator5)"
+    "\n",
+    "indicator6 = indicator5.set_markings([TLP_GREEN, marking_definition])\n",
+    "print(indicator6.serialize(pretty=True))"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The markings on an object can be replaced with a different set of markings:"
+    "STIX objects can also be cleared of all markings with [clear_markings()](../api/stix2.markings.rst#stix2.markings.clear_markings):"
    ]
   },
   {
@@ -939,8 +1095,13 @@
     {
      "data": {
       "text/html": [
-       "<style type=\"text/css\">.highlight .hll { background-color: #ffffcc }\n",
+       "<style type=\"text/css\">pre { line-height: 125%; }\n",
-       ".highlight  { background: #f8f8f8; }\n",
+       "td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       ".highlight .hll { background-color: #ffffcc }\n",
+       ".highlight { background: #f8f8f8; }\n",
        ".highlight .c { color: #408080; font-style: italic } /* Comment */\n",
        ".highlight .err { border: 1px solid #FF0000 } /* Error */\n",
        ".highlight .k { color: #008000; font-weight: bold } /* Keyword */\n",
@@ -1010,17 +1171,13 @@
        ".highlight .il { color: #666666 } /* Literal.Number.Integer.Long */</style><div class=\"highlight\"><pre><span></span><span class=\"p\">{</span>\n",
        "    <span class=\"nt\">&quot;type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;spec_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--46498844-7689-4e7b-be25-b119d8401159&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--a315ce0b-1211-478e-812a-cd6d3eecc3c1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T20:55:56.088861Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T13:59:48.911595Z&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:21:47.703212Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:00:06.512465Z&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;[file:hashes.md5 = &#39;d41d8cd98f00b204e9800998ecf8427e&#39;]&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern_type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;stix&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T20:55:56.088861Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T13:59:48.911595Z&quot;</span>\n",
-       "    <span class=\"nt\">&quot;object_marking_refs&quot;</span><span class=\"p\">:</span> <span class=\"p\">[</span>\n",
-       "        <span class=\"s2\">&quot;marking-definition--9a4efc30-a7ac-42d0-8776-16f390a0fd44&quot;</span><span class=\"p\">,</span>\n",
-       "        <span class=\"s2\">&quot;marking-definition--34098fce-860f-48ae-8e50-ebd3cc5e41da&quot;</span>\n",
-       "    <span class=\"p\">]</span>\n",
        "<span class=\"p\">}</span>\n",
        "</pre></div>\n"
       ],
@@ -1033,121 +1190,9 @@
      "output_type": "execute_result"
     }
    ],
-   "source": [
-    "from stix2 import TLP_GREEN\n",
-    "\n",
-    "indicator6 = indicator5.set_markings([TLP_GREEN, marking_definition])\n",
-    "print(indicator6)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "STIX objects can also be cleared of all markings with [clear_markings()](../api/stix2.markings.rst#stix2.markings.clear_markings):"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 13,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<style type=\"text/css\">.highlight .hll { background-color: #ffffcc }\n",
-       ".highlight  { background: #f8f8f8; }\n",
-       ".highlight .c { color: #408080; font-style: italic } /* Comment */\n",
-       ".highlight .err { border: 1px solid #FF0000 } /* Error */\n",
-       ".highlight .k { color: #008000; font-weight: bold } /* Keyword */\n",
-       ".highlight .o { color: #666666 } /* Operator */\n",
-       ".highlight .ch { color: #408080; font-style: italic } /* Comment.Hashbang */\n",
-       ".highlight .cm { color: #408080; font-style: italic } /* Comment.Multiline */\n",
-       ".highlight .cp { color: #BC7A00 } /* Comment.Preproc */\n",
-       ".highlight .cpf { color: #408080; font-style: italic } /* Comment.PreprocFile */\n",
-       ".highlight .c1 { color: #408080; font-style: italic } /* Comment.Single */\n",
-       ".highlight .cs { color: #408080; font-style: italic } /* Comment.Special */\n",
-       ".highlight .gd { color: #A00000 } /* Generic.Deleted */\n",
-       ".highlight .ge { font-style: italic } /* Generic.Emph */\n",
-       ".highlight .gr { color: #FF0000 } /* Generic.Error */\n",
-       ".highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */\n",
-       ".highlight .gi { color: #00A000 } /* Generic.Inserted */\n",
-       ".highlight .go { color: #888888 } /* Generic.Output */\n",
-       ".highlight .gp { color: #000080; font-weight: bold } /* Generic.Prompt */\n",
-       ".highlight .gs { font-weight: bold } /* Generic.Strong */\n",
-       ".highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */\n",
-       ".highlight .gt { color: #0044DD } /* Generic.Traceback */\n",
-       ".highlight .kc { color: #008000; font-weight: bold } /* Keyword.Constant */\n",
-       ".highlight .kd { color: #008000; font-weight: bold } /* Keyword.Declaration */\n",
-       ".highlight .kn { color: #008000; font-weight: bold } /* Keyword.Namespace */\n",
-       ".highlight .kp { color: #008000 } /* Keyword.Pseudo */\n",
-       ".highlight .kr { color: #008000; font-weight: bold } /* Keyword.Reserved */\n",
-       ".highlight .kt { color: #B00040 } /* Keyword.Type */\n",
-       ".highlight .m { color: #666666 } /* Literal.Number */\n",
-       ".highlight .s { color: #BA2121 } /* Literal.String */\n",
-       ".highlight .na { color: #7D9029 } /* Name.Attribute */\n",
-       ".highlight .nb { color: #008000 } /* Name.Builtin */\n",
-       ".highlight .nc { color: #0000FF; font-weight: bold } /* Name.Class */\n",
-       ".highlight .no { color: #880000 } /* Name.Constant */\n",
-       ".highlight .nd { color: #AA22FF } /* Name.Decorator */\n",
-       ".highlight .ni { color: #999999; font-weight: bold } /* Name.Entity */\n",
-       ".highlight .ne { color: #D2413A; font-weight: bold } /* Name.Exception */\n",
-       ".highlight .nf { color: #0000FF } /* Name.Function */\n",
-       ".highlight .nl { color: #A0A000 } /* Name.Label */\n",
-       ".highlight .nn { color: #0000FF; font-weight: bold } /* Name.Namespace */\n",
-       ".highlight .nt { color: #008000; font-weight: bold } /* Name.Tag */\n",
-       ".highlight .nv { color: #19177C } /* Name.Variable */\n",
-       ".highlight .ow { color: #AA22FF; font-weight: bold } /* Operator.Word */\n",
-       ".highlight .w { color: #bbbbbb } /* Text.Whitespace */\n",
-       ".highlight .mb { color: #666666 } /* Literal.Number.Bin */\n",
-       ".highlight .mf { color: #666666 } /* Literal.Number.Float */\n",
-       ".highlight .mh { color: #666666 } /* Literal.Number.Hex */\n",
-       ".highlight .mi { color: #666666 } /* Literal.Number.Integer */\n",
-       ".highlight .mo { color: #666666 } /* Literal.Number.Oct */\n",
-       ".highlight .sa { color: #BA2121 } /* Literal.String.Affix */\n",
-       ".highlight .sb { color: #BA2121 } /* Literal.String.Backtick */\n",
-       ".highlight .sc { color: #BA2121 } /* Literal.String.Char */\n",
-       ".highlight .dl { color: #BA2121 } /* Literal.String.Delimiter */\n",
-       ".highlight .sd { color: #BA2121; font-style: italic } /* Literal.String.Doc */\n",
-       ".highlight .s2 { color: #BA2121 } /* Literal.String.Double */\n",
-       ".highlight .se { color: #BB6622; font-weight: bold } /* Literal.String.Escape */\n",
-       ".highlight .sh { color: #BA2121 } /* Literal.String.Heredoc */\n",
-       ".highlight .si { color: #BB6688; font-weight: bold } /* Literal.String.Interpol */\n",
-       ".highlight .sx { color: #008000 } /* Literal.String.Other */\n",
-       ".highlight .sr { color: #BB6688 } /* Literal.String.Regex */\n",
-       ".highlight .s1 { color: #BA2121 } /* Literal.String.Single */\n",
-       ".highlight .ss { color: #19177C } /* Literal.String.Symbol */\n",
-       ".highlight .bp { color: #008000 } /* Name.Builtin.Pseudo */\n",
-       ".highlight .fm { color: #0000FF } /* Name.Function.Magic */\n",
-       ".highlight .vc { color: #19177C } /* Name.Variable.Class */\n",
-       ".highlight .vg { color: #19177C } /* Name.Variable.Global */\n",
-       ".highlight .vi { color: #19177C } /* Name.Variable.Instance */\n",
-       ".highlight .vm { color: #19177C } /* Name.Variable.Magic */\n",
-       ".highlight .il { color: #666666 } /* Literal.Number.Integer.Long */</style><div class=\"highlight\"><pre><span></span><span class=\"p\">{</span>\n",
-       "    <span class=\"nt\">&quot;type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;spec_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--46498844-7689-4e7b-be25-b119d8401159&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T20:55:56.088861Z&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:21:53.287178Z&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;pattern&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;[file:hashes.md5 = &#39;d41d8cd98f00b204e9800998ecf8427e&#39;]&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;pattern_type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;stix&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;pattern_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T20:55:56.088861Z&quot;</span>\n",
-       "<span class=\"p\">}</span>\n",
-       "</pre></div>\n"
-      ],
-      "text/plain": [
-       "<IPython.core.display.HTML object>"
-      ]
-     },
-     "execution_count": 13,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
    "source": [
     "indicator7 = indicator5.clear_markings()\n",
-    "print(indicator7)"
+    "print(indicator7.serialize(pretty=True))"
    ]
   },
   {
@@ -1168,17 +1213,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "['marking-definition--9a4efc30-a7ac-42d0-8776-16f390a0fd44',\n",
+       "['marking-definition--34098fce-860f-48ae-8e50-ebd3cc5e41da',\n",
-       " 'marking-definition--34098fce-860f-48ae-8e50-ebd3cc5e41da']"
+       " 'marking-definition--4b8e86b5-d505-46a4-91b4-a8db17f4ff4d']"
       ]
      },
-     "execution_count": 14,
+     "execution_count": 13,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1196,7 +1241,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
@@ -1205,7 +1250,7 @@
        "['marking-definition--613f2e26-407d-48c7-9eca-b8e91df99dc9']"
       ]
      },
-     "execution_count": 15,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1225,7 +1270,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [
     {
@@ -1234,7 +1279,7 @@
        "['marking-definition--613f2e26-407d-48c7-9eca-b8e91df99dc9']"
       ]
      },
-     "execution_count": 16,
+     "execution_count": 15,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1250,6 +1295,26 @@
     "Finally, you may also check if an object is marked by a specific markings. Again, for granular markings, pass in the selector or list of selectors."
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 16,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "indicator.is_marked(TLP_AMBER.id)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 17,
@@ -1266,33 +1331,13 @@
      "output_type": "execute_result"
     }
    ],
-   "source": [
-    "indicator.is_marked(TLP_AMBER.id)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 18,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "True"
-      ]
-     },
-     "execution_count": 18,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
    "source": [
     "malware.is_marked(TLP_WHITE.id, 'name')"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 18,
    "metadata": {
     "scrolled": true
    },
@@ -1303,7 +1348,7 @@
        "False"
       ]
      },
-     "execution_count": 19,
+     "execution_count": 18,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1323,14 +1368,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": 19,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/html": [
-       "<style type=\"text/css\">.highlight .hll { background-color: #ffffcc }\n",
+       "<style type=\"text/css\">pre { line-height: 125%; }\n",
-       ".highlight  { background: #f8f8f8; }\n",
+       "td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       ".highlight .hll { background-color: #ffffcc }\n",
+       ".highlight { background: #f8f8f8; }\n",
        ".highlight .c { color: #408080; font-style: italic } /* Comment */\n",
        ".highlight .err { border: 1px solid #FF0000 } /* Error */\n",
        ".highlight .k { color: #008000; font-weight: bold } /* Keyword */\n",
@@ -1400,9 +1450,9 @@
        ".highlight .il { color: #666666 } /* Literal.Number.Integer.Long */</style><div class=\"highlight\"><pre><span></span><span class=\"p\">{</span>\n",
        "    <span class=\"nt\">&quot;type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;spec_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--f4004de9-a6d9-4c7b-823e-3d8199173c09&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--a2fd263a-ec46-4fff-84af-27419f0b9f15&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:35:08.630228Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:02:31.991141Z&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:35:08.630228Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:02:31.991141Z&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;description&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;Una descripcion sobre este indicador&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;indicator_types&quot;</span><span class=\"p\">:</span> <span class=\"p\">[</span>\n",
        "        <span class=\"s2\">&quot;malware&quot;</span>\n",
@@ -1410,7 +1460,7 @@
        "    <span class=\"nt\">&quot;pattern&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;[file:hashes.md5 = &#39;d41d8cd98f00b204e9800998ecf8427e&#39;]&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern_type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;stix&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:35:08.630228Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:02:31.991141Z&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;object_marking_refs&quot;</span><span class=\"p\">:</span> <span class=\"p\">[</span>\n",
        "        <span class=\"s2\">&quot;marking-definition--f88d31f6-486f-44da-b317-01333bde0b82&quot;</span>\n",
        "    <span class=\"p\">],</span>\n",
@@ -1435,15 +1485,20 @@
        "<IPython.core.display.HTML object>"
       ]
      },
-     "execution_count": 20,
+     "execution_count": 19,
      "metadata": {},
      "output_type": "execute_result"
     },
     {
      "data": {
       "text/html": [
-       "<style type=\"text/css\">.highlight .hll { background-color: #ffffcc }\n",
+       "<style type=\"text/css\">pre { line-height: 125%; }\n",
-       ".highlight  { background: #f8f8f8; }\n",
+       "td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       ".highlight .hll { background-color: #ffffcc }\n",
+       ".highlight { background: #f8f8f8; }\n",
        ".highlight .c { color: #408080; font-style: italic } /* Comment */\n",
        ".highlight .err { border: 1px solid #FF0000 } /* Error */\n",
        ".highlight .k { color: #008000; font-weight: bold } /* Keyword */\n",
@@ -1517,15 +1572,20 @@
        "<IPython.core.display.HTML object>"
       ]
      },
-     "execution_count": 20,
+     "execution_count": 19,
      "metadata": {},
      "output_type": "execute_result"
     },
     {
      "data": {
       "text/html": [
-       "<style type=\"text/css\">.highlight .hll { background-color: #ffffcc }\n",
+       "<style type=\"text/css\">pre { line-height: 125%; }\n",
-       ".highlight  { background: #f8f8f8; }\n",
+       "td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       ".highlight .hll { background-color: #ffffcc }\n",
+       ".highlight { background: #f8f8f8; }\n",
        ".highlight .c { color: #408080; font-style: italic } /* Comment */\n",
        ".highlight .err { border: 1px solid #FF0000 } /* Error */\n",
        ".highlight .k { color: #008000; font-weight: bold } /* Keyword */\n",
@@ -1599,15 +1659,20 @@
        "<IPython.core.display.HTML object>"
       ]
      },
-     "execution_count": 20,
+     "execution_count": 19,
      "metadata": {},
      "output_type": "execute_result"
     },
     {
      "data": {
       "text/html": [
-       "<style type=\"text/css\">.highlight .hll { background-color: #ffffcc }\n",
+       "<style type=\"text/css\">pre { line-height: 125%; }\n",
-       ".highlight  { background: #f8f8f8; }\n",
+       "td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       ".highlight .hll { background-color: #ffffcc }\n",
+       ".highlight { background: #f8f8f8; }\n",
        ".highlight .c { color: #408080; font-style: italic } /* Comment */\n",
        ".highlight .err { border: 1px solid #FF0000 } /* Error */\n",
        ".highlight .k { color: #008000; font-weight: bold } /* Keyword */\n",
@@ -1681,7 +1746,7 @@
        "<IPython.core.display.HTML object>"
       ]
      },
-     "execution_count": 20,
+     "execution_count": 19,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1706,7 +1771,7 @@
     "        }\n",
     "    ]\n",
     ")\n",
-    "print(v21_indicator)\n",
+    "print(v21_indicator.serialize(pretty=True))\n",
     "\n",
     "# Gets both lang and marking_ref markings for 'description'\n",
     "print(v21_indicator.get_markings('description'))\n",
@@ -1733,8 +1798,13 @@
     {
      "data": {
       "text/html": [
-       "<style type=\"text/css\">.highlight .hll { background-color: #ffffcc }\n",
+       "<style type=\"text/css\">pre { line-height: 125%; }\n",
-       ".highlight  { background: #f8f8f8; }\n",
+       "td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       ".highlight .hll { background-color: #ffffcc }\n",
+       ".highlight { background: #f8f8f8; }\n",
        ".highlight .c { color: #408080; font-style: italic } /* Comment */\n",
        ".highlight .err { border: 1px solid #FF0000 } /* Error */\n",
        ".highlight .k { color: #008000; font-weight: bold } /* Keyword */\n",
@@ -1804,9 +1874,9 @@
        ".highlight .il { color: #666666 } /* Literal.Number.Integer.Long */</style><div class=\"highlight\"><pre><span></span><span class=\"p\">{</span>\n",
        "    <span class=\"nt\">&quot;type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;spec_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--f4004de9-a6d9-4c7b-823e-3d8199173c09&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--a2fd263a-ec46-4fff-84af-27419f0b9f15&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:35:08.630228Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:02:31.991141Z&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:35:14.54482Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:03:11.817032Z&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;description&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;Una descripcion sobre este indicador&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;indicator_types&quot;</span><span class=\"p\">:</span> <span class=\"p\">[</span>\n",
        "        <span class=\"s2\">&quot;malware&quot;</span>\n",
@@ -1814,7 +1884,7 @@
        "    <span class=\"nt\">&quot;pattern&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;[file:hashes.md5 = &#39;d41d8cd98f00b204e9800998ecf8427e&#39;]&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern_type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;stix&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:35:08.630228Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:02:31.991141Z&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;object_marking_refs&quot;</span><span class=\"p\">:</span> <span class=\"p\">[</span>\n",
        "        <span class=\"s2\">&quot;marking-definition--f88d31f6-486f-44da-b317-01333bde0b82&quot;</span>\n",
        "    <span class=\"p\">]</span>\n",
@@ -1831,7 +1901,8 @@
     }
    ],
    "source": [
-    "print(v21_indicator.clear_markings(\"description\"))  # By default, both types of markings will be removed"
+    "# By default, both types of markings will be removed\n",
+    "print(v21_indicator.clear_markings(\"description\").serialize(pretty=True))"
    ]
   },
   {
@@ -1842,8 +1913,13 @@
     {
      "data": {
       "text/html": [
-       "<style type=\"text/css\">.highlight .hll { background-color: #ffffcc }\n",
+       "<style type=\"text/css\">pre { line-height: 125%; }\n",
-       ".highlight  { background: #f8f8f8; }\n",
+       "td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       ".highlight .hll { background-color: #ffffcc }\n",
+       ".highlight { background: #f8f8f8; }\n",
        ".highlight .c { color: #408080; font-style: italic } /* Comment */\n",
        ".highlight .err { border: 1px solid #FF0000 } /* Error */\n",
        ".highlight .k { color: #008000; font-weight: bold } /* Keyword */\n",
@@ -1913,9 +1989,9 @@
        ".highlight .il { color: #666666 } /* Literal.Number.Integer.Long */</style><div class=\"highlight\"><pre><span></span><span class=\"p\">{</span>\n",
        "    <span class=\"nt\">&quot;type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;spec_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--f4004de9-a6d9-4c7b-823e-3d8199173c09&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--a2fd263a-ec46-4fff-84af-27419f0b9f15&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:35:08.630228Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:02:31.991141Z&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:35:39.298138Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:03:24.701927Z&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;description&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;Una descripcion sobre este indicador&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;indicator_types&quot;</span><span class=\"p\">:</span> <span class=\"p\">[</span>\n",
        "        <span class=\"s2\">&quot;malware&quot;</span>\n",
@@ -1923,7 +1999,7 @@
        "    <span class=\"nt\">&quot;pattern&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;[file:hashes.md5 = &#39;d41d8cd98f00b204e9800998ecf8427e&#39;]&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern_type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;stix&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:35:08.630228Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:02:31.991141Z&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;object_marking_refs&quot;</span><span class=\"p\">:</span> <span class=\"p\">[</span>\n",
        "        <span class=\"s2\">&quot;marking-definition--f88d31f6-486f-44da-b317-01333bde0b82&quot;</span>\n",
        "    <span class=\"p\">],</span>\n",
@@ -1949,7 +2025,7 @@
    ],
    "source": [
     "# If lang is False, no lang markings will be removed\n",
-    "print(v21_indicator.clear_markings(\"description\", lang=False))"
+    "print(v21_indicator.clear_markings(\"description\", lang=False).serialize(pretty=True))"
    ]
   },
   {
@@ -1960,8 +2036,13 @@
     {
      "data": {
       "text/html": [
-       "<style type=\"text/css\">.highlight .hll { background-color: #ffffcc }\n",
+       "<style type=\"text/css\">pre { line-height: 125%; }\n",
-       ".highlight  { background: #f8f8f8; }\n",
+       "td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }\n",
+       "td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       "span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }\n",
+       ".highlight .hll { background-color: #ffffcc }\n",
+       ".highlight { background: #f8f8f8; }\n",
        ".highlight .c { color: #408080; font-style: italic } /* Comment */\n",
        ".highlight .err { border: 1px solid #FF0000 } /* Error */\n",
        ".highlight .k { color: #008000; font-weight: bold } /* Keyword */\n",
@@ -2031,9 +2112,9 @@
        ".highlight .il { color: #666666 } /* Literal.Number.Integer.Long */</style><div class=\"highlight\"><pre><span></span><span class=\"p\">{</span>\n",
        "    <span class=\"nt\">&quot;type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;spec_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--f4004de9-a6d9-4c7b-823e-3d8199173c09&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;id&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;indicator--a2fd263a-ec46-4fff-84af-27419f0b9f15&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:35:08.630228Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;created&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:02:31.991141Z&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:35:42.684794Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;modified&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:03:29.751985Z&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;description&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;Una descripcion sobre este indicador&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;indicator_types&quot;</span><span class=\"p\">:</span> <span class=\"p\">[</span>\n",
        "        <span class=\"s2\">&quot;malware&quot;</span>\n",
@@ -2041,7 +2122,7 @@
        "    <span class=\"nt\">&quot;pattern&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;[file:hashes.md5 = &#39;d41d8cd98f00b204e9800998ecf8427e&#39;]&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern_type&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;stix&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;pattern_version&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2.1&quot;</span><span class=\"p\">,</span>\n",
-       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2020-06-24T21:35:08.630228Z&quot;</span><span class=\"p\">,</span>\n",
+       "    <span class=\"nt\">&quot;valid_from&quot;</span><span class=\"p\">:</span> <span class=\"s2\">&quot;2021-04-09T14:02:31.991141Z&quot;</span><span class=\"p\">,</span>\n",
        "    <span class=\"nt\">&quot;object_marking_refs&quot;</span><span class=\"p\">:</span> <span class=\"p\">[</span>\n",
        "        <span class=\"s2\">&quot;marking-definition--f88d31f6-486f-44da-b317-01333bde0b82&quot;</span>\n",
        "    <span class=\"p\">],</span>\n",
@@ -2067,7 +2148,7 @@
    ],
    "source": [
     "# If marking_ref is False, no marking-definition markings will be removed\n",
-    "print(v21_indicator.clear_markings(\"description\", marking_ref=False))"
+    "print(v21_indicator.clear_markings(\"description\", marking_ref=False).serialize(pretty=True))"
    ]
   }
  ],
@@ -2087,7 +2168,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.0a6"
+   "version": "3.9.2"
   }
  },
  "nbformat": 4,

docs/guide/patterns.ipynb

@@ -1502,7 +1502,7 @@
     "\n",
     "ece14 = ObservationExpression(EqualityComparisonExpression(ObjectPath(\"file\", [\"name\"]), \"$$t00rzch$$.elf\"))\n",
     "ind = Indicator(name=\"Cryptotorch\", pattern_type=\"stix\", pattern=ece14)\n",
-    "print(ind)"
+    "print(ind.serialize(pretty=True))"
    ]
   }
  ],
@@ -1522,7 +1522,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.0a6"
+   "version": "3.9.2"
   }
  },
  "nbformat": 4,

docs/guide/serializing.ipynb

@@ -183,7 +183,7 @@
     "---\n",
     "**New in 3.0.0:** \n",
     "\n",
-    "Calling `str()` on a STIX object will call `serialize()` without any formatting options. The change was made to address the performance penalty induced by unknowingly calling with the pretty formatted option. As shown above, to get effect `str()` would in the past versions of the library use the method directly and pass the pretty argument directly `serialize(pretty=True)`.\n",
+    "Calling `str()` on a STIX object will call `serialize()` without any formatting options. The change was made to address the performance penalty induced by unknowingly calling with the pretty formatted option. As shown above, to get the same effect as `str()` had in past versions of the library, use the method directly and pass in the pretty argument `serialize(pretty=True)`.\n",
     "\n",
     "---\n",
     "\n",

stix2/base.py

@@ -126,7 +126,6 @@ class _STIXBase(collections.abc.Mapping):
             if ext_found is False:
                 raise ExtraPropertiesError(cls, extra_kwargs)
 
-        # because allow_custom is true, any extra kwargs are custom
         if custom_props or extra_kwargs:
             self._allow_custom = True
             if isinstance(self, stix2.v21._STIXBase21):
@@ -153,7 +152,8 @@ class _STIXBase(collections.abc.Mapping):
         if missing_kwargs:
             new_ext_check = (
                 bool(getattr(self, "extension_type", None))
-            ) and issubclass(cls, stix2.v21._Extension)
+                and issubclass(cls, stix2.v21._Extension)
+            )
             if new_ext_check is False:
                 raise MissingPropertiesError(cls, missing_kwargs)
 

stix2/parsing.py

@@ -87,11 +87,14 @@ def dict_to_stix2(stix_dict, allow_custom=False, version=None):
             # be parsed into STIX object, returned as is
             return stix_dict
         for key_id, ext_def in stix_dict.get('extensions', {}).items():
-            if key_id.startswith('extension-definition--') and ext_def.get('extension_type', None):
+            if (
+                key_id.startswith('extension-definition--') and
+                'property-extension' not in ext_def.get('extension_type', '')
+            ):
                 # prevents ParseError for unregistered objects when
-                # 'is_new_object' or 'is_extension_so' are set to True and allow_custom=False
+                # allow_custom=False and the extension defines a new object
                 return stix_dict
-        raise ParseError("Can't parse unknown object type '%s'! For custom types, use the CustomObject decorator." % stix_dict['type'])
+        raise ParseError("Can't parse unknown object type '%s'! For custom types, use the CustomObject decorator." % obj_type)
 
     return obj_class(allow_custom=allow_custom, **stix_dict)
 

stix2/registry.py

@@ -76,8 +76,4 @@ def class_for_type(stix_type, stix_version, category=None):
                 cat_map["extensions"].get(stix_type)
             )
 
-    # Left "observable-extensions" out; it has a different
-    # substructure.  A version->category->type lookup would result
-    # in another map, not a class.  So it doesn't fit the pattern.
-
     return cls