diff --git a/python39.yaml b/python39.yaml
index 7990482..954815a 100644
--- a/python39.yaml
+++ b/python39.yaml
@@ -54,6 +54,12 @@ data:
                 # # pip
                 # %_without_doc 1
 
+                # === Bootstrap phase 2 ===
+                #
+                # %python3_pkgversion 39
+                # # setuptools, pip, ...
+                # %_without_tests 1
+
 
             # Macros bootstrapping info:
             #   Only the macros that are below the `macros: |` declaration are
@@ -67,10 +73,10 @@ data:
             #   therefore it's safer to just move them out of the macros
             #   section entirely to avoid possible issues.
             macros: |
-                # === Bootstrap phase 2 ===
+                # === Bootstrap phase 3 ===
                 #
                 %python3_pkgversion 39
-                # setuptools, pip, ...
+                # scipy needs pybind11 to build and pybind11 needs scipy for tests
                 %_without_tests 1
 
     components:
@@ -97,74 +103,201 @@ data:
 
             # === Bootstrap phase 2 ===
             #
+            # python3x-setuptools:
+            #     rationale: Packaging tool
+            #     ref: 1950ae3d8549d4df835b6e31337bebd9a40bf4f8
+            #     buildorder: 10
+            # python3x-pyparsing:
+            #     rationale: Python component
+            #     ref: ad9334c8fb4a6a6e24252c4a94f64523044b0368
+            #     buildorder: 20
+            # python39:
+            #     rationale: The main Python interpreter
+            #     ref: 93a1c0a50478623f84220798338b4d66a2e7117c
+            #     buildorder: 30
+            # python-wheel:
+            #     rationale: Packaging tool
+            #     ref: 1d3137dab7dbb7c7fa4526224de74ab47cadbd95
+            #     buildorder: 40
+            # python3x-pip:
+            #     rationale: Packaging tool
+            #     ref: 0bf48e6304b1048952635f8811b3f8992347623b
+            #     buildorder: 40
+            # python3x-six:
+            #     rationale: Python component
+            #     ref: 3930eca3dcbfbe7c80ab9c0f4d385e3f818016eb
+            #     buildorder: 40
+            # python-py:
+            #     rationale: Python component
+            #     ref: f98dc1297bfd38a5356aee346c59259cd983bfaa
+            #     buildorder: 40
+            # python-chardet:
+            #     rationale: Python component
+            #     # stream branch shared with python38 module
+            #     ref: 04b5d1be6d2e14ece3a43caa87b79216ea35b65a
+            #     buildorder: 40
+            # python-attrs:
+            #     rationale: Python component
+            #     ref: b68e1e37d4944f9a20e452bb3596e5f75b9506be
+            #     buildorder: 40
+            # python-pluggy:
+            #     rationale: Python component
+            #     ref: 2abffaab2ce5b6a5e0121442bdd5a49eb4c4f752
+            #     buildorder: 40
+            # python-pysocks:
+            #     rationale: Python component
+            #     # stream branch shared with python38 module
+            #     ref: 483216203ae75373f15aea373c80ee0585c13e63
+            #     buildorder: 40
+            # python-wcwidth:
+            #     rationale: Python component
+            #     ref: d45e8c1e3fcd02f21d6bdd008f877380c1dd69c1
+            #     buildorder: 40
+            # python-packaging:
+            #     rationale: Python component
+            #     ref: d6dd7925507609cedacc346a2793842dfbdcdf72
+            #     buildorder: 40
+            # python-toml:
+            #     rationale: Python component
+            #     ref: dc3e570c0f28ba1c9b9bbca871b122e0a5f8a2ff
+            #     buildorder: 40
+            # python-iniconfig:
+            #     rationale: Python component
+            #     ref: f707fca709c2a1d006dcff691dfa2b9b648ecb7f
+            #     buildorder: 40
+            # python-more-itertools:
+            #     rationale: Python component
+            #     ref: 4c7d27c844b65549cf4162977488b7b63288b377
+            #     buildorder: 50
+            # pytest:
+            #     rationale: Python component
+            #     ref: 0e0110864115c99e4e69ed78021a478fac350f33
+            #     buildorder: 60
+
+
+            # === Bootstrap phase 3/4 ===
+            # For bootstrap phase 3 uncomment all `buildorder:` lines below,
+            # for bootstrap phase 4 comment them out.
+            #
             python3x-setuptools:
                 rationale: Packaging tool
                 ref: 1950ae3d8549d4df835b6e31337bebd9a40bf4f8
-                buildorder: 10
             python3x-pyparsing:
                 rationale: Python component
                 ref: ad9334c8fb4a6a6e24252c4a94f64523044b0368
-                buildorder: 20
             python39:
                 rationale: The main Python interpreter
                 ref: 93a1c0a50478623f84220798338b4d66a2e7117c
-                buildorder: 30
             python-wheel:
                 rationale: Packaging tool
                 ref: 1d3137dab7dbb7c7fa4526224de74ab47cadbd95
-                buildorder: 40
             python3x-pip:
                 rationale: Packaging tool
                 ref: 0bf48e6304b1048952635f8811b3f8992347623b
-                buildorder: 40
+
             python3x-six:
                 rationale: Python component
                 ref: 3930eca3dcbfbe7c80ab9c0f4d385e3f818016eb
-                buildorder: 40
             python-py:
                 rationale: Python component
                 ref: f98dc1297bfd38a5356aee346c59259cd983bfaa
-                buildorder: 40
             python-chardet:
                 rationale: Python component
                 # stream branch shared with python38 module
                 ref: 04b5d1be6d2e14ece3a43caa87b79216ea35b65a
-                buildorder: 40
             python-attrs:
                 rationale: Python component
                 ref: b68e1e37d4944f9a20e452bb3596e5f75b9506be
-                buildorder: 40
             python-pluggy:
                 rationale: Python component
                 ref: 2abffaab2ce5b6a5e0121442bdd5a49eb4c4f752
-                buildorder: 40
             python-pysocks:
                 rationale: Python component
                 # stream branch shared with python38 module
                 ref: 483216203ae75373f15aea373c80ee0585c13e63
-                buildorder: 40
             python-wcwidth:
                 rationale: Python component
                 ref: d45e8c1e3fcd02f21d6bdd008f877380c1dd69c1
-                buildorder: 40
             python-packaging:
                 rationale: Python component
                 ref: d6dd7925507609cedacc346a2793842dfbdcdf72
-                buildorder: 40
             python-toml:
                 rationale: Python component
                 ref: dc3e570c0f28ba1c9b9bbca871b122e0a5f8a2ff
-                buildorder: 40
             python-iniconfig:
                 rationale: Python component
                 ref: f707fca709c2a1d006dcff691dfa2b9b648ecb7f
-                buildorder: 40
             python-more-itertools:
                 rationale: Python component
                 ref: 4c7d27c844b65549cf4162977488b7b63288b377
-                buildorder: 50
             pytest:
                 rationale: Python component
                 ref: 0e0110864115c99e4e69ed78021a478fac350f33
-                buildorder: 60
+
+            python-idna:
+                rationale: Python component
+                ref: 96079b9187a3c449211a2dc1a4e910ef9956b7e9
+            python-urllib3:
+                rationale: Python component
+                ref: 6b6e02d630b786437deed074d421051cc2acbe87
+            Cython:
+                rationale: Python component
+                ref: 8c789216e7ce6b5e929c5046a27d5d890423c750
+            python-ply:
+                rationale: Python component
+                # stream branch shared with python38 module
+                ref: f113e7017224318a0e816f6e78f938187ff60515
+            python-psutil:
+                rationale: Python component
+                ref: b24769857571306e8bb21f72c53c1ef1a6fb95f6
+            python-psycopg2:
+                rationale: Python component
+                ref: 439d6fa4527303c38f65ae247c709410adb5821a
+            mod_wsgi:
+                rationale: Python component
+                ref: 83f89e967cf6729d4e78591b29ebde950ff12aea
+            python-requests:
+                rationale: Python component
+                ref: f99a3f5bab770a5fea956ceef8e9d0cd506b6379
+                buildorder: 10
+            numpy:
+                rationale: Python component
+                ref: 593d45b8a06077089786e5c3818950d295e85871
+                buildorder: 10
+            PyYAML:
+                rationale: Python component
+                ref: fadfcf8207e37e3910989e51f9d2e2ebcf783051
+                buildorder: 10
+            python-pycparser:
+                rationale: Python component
+                ref: ca7845af04898c3f98db25937fa93a58e5166cf4
+                buildorder: 10
+            python-lxml:
+                rationale: Python component
+                ref: 594c36cb17094416e72ceb7c1b9aefa9bc2857b7
+                buildorder: 10
+            python-cffi:
+                rationale: Python component
+                ref: b66960cca0cb1074520655088cae60899bd8fd00
+                buildorder: 20
+            pybind11:
+                rationale: Python component
+                ref: c5ded38bf8d331512fc09d82e8621fbf288f221f
+                # needs numpy
+                buildorder: 20
+            scipy:
+                rationale: Python component
+                ref: 0c42ffd27fafcf93fe7ca76033dedf8f4052ddcc
+                # needs pybind11
+                buildorder: 30
+            python-cryptography:
+                rationale: Python component
+                ref: e304a6883592ff881d6396fcd4a95c9f62eab810
+                # needs cffi
+                buildorder: 30
+            python-PyMySQL:
+                rationale: Python component
+                ref: dc5bc3753d271278f5da87a774ce58e924ed66b8
+                # needs cryptography
+                buildorder: 40
 ...