studio2ped 0.2.0__tar.gz → 0.2.1__tar.gz

{studio2ped-0.2.0 → studio2ped-0.2.1}/CHANGELOG.md

@@ -1,5 +1,26 @@
 # Changelog
 
+## 0.2.1
+
+- A parent marked G is a gestational carrier, and is not written as a genetic
+  parent. Since the 2025 correction to the pedigree nomenclature (Steinhaus
+  French, Bennett and Resta, *J Genet Couns* 2025;34(2):e2020), G marks a
+  gestational carrier, and Pedigree Studio draws G where it used to draw S.
+  S, which older drawings use, still means the same.
+- The note says "gestational carrier" and gives the mark (G or S), not
+  "surrogate": the corrected nomenclature keeps "surrogate" for a woman who
+  gives the egg and carries the pregnancy, who is a genetic parent.
+- A symbol divided into thirds, which Pedigree Studio now draws for three
+  conditions, gives each of its colours as a condition the person has, as
+  quarters do.
+- The "no children" and "infertility" symbols no longer count when a row is
+  numbered. The nomenclature numbers individuals (Bennett et al., *J Genet
+  Couns* 2022;31(6):1238-48) and these symbols are not people, so Pedigree
+  Studio now gives them no number, and studio2ped numbers only people too:
+  someone to the right of one of these symbols in the same row has a number
+  one lower than before (II-3 rather than II-4), and a row with nothing but
+  these symbols is not a generation.
+
 ## 0.2.0
 
 - People are now identified by their pedigree numbers (I-1, II-3 and so on),

{studio2ped-0.2.0/studio2ped.egg-info → studio2ped-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: studio2ped
-Version: 0.2.0
+Version: 0.2.1
 Summary: Convert Pedigree Studio session JSON to PED/MPED pedigree files
 Author-email: Tim Hearn <tjh70@cam.ac.uk>
 License-Expression: MIT
@@ -99,11 +99,12 @@ The converter reads a Pedigree Studio session file and:
 4. **Gives genetic parents only.** The father and mother columns of a PED
    file are genetic parents. A child joined to a couple by a dashed line (an
    adoption) gets 0 for that couple, and so does the place of a parent marked
-   S (a gestational carrier), with a note in each case; a parent marked D (a
-   donor) is a genetic parent. studio2ga4gh's PED-style pedigree gives the
-   same.
+   G (a gestational carrier), with a note in each case; a parent marked D (a
+   donor) is a genetic parent. Drawings made before the 2025 correction to the
+   pedigree nomenclature mark a gestational carrier S, which is read the same
+   way. studio2ga4gh's PED-style pedigree gives the same.
 5. **Extracts phenotypes** from the colour key: solid fills, half fills,
-   quartered fills and shading patterns are all recognised.
+   symbols in thirds or quarters, and shading patterns are all recognised.
 6. **Detects carrier notation**: centre dots (●) and half-filled symbols mark
    carriers.
 7. **Chooses the format**:
@@ -136,9 +137,10 @@ would be `0`, the person is given their pedigree number instead, and a note
 says so.
 
 Pedigree numbers follow the drawing, as in Pedigree Studio: a new generation
-starts 80 pixels or more below the first symbol of the generation above, and
-the "no children" and "infertility" symbols are counted in their row, even
-though they are not written to the file.
+starts 80 pixels or more below the first person of the generation above, and
+each generation is numbered from the left. Only people are numbered: the "no
+children" and "infertility" symbols are not people, so they have no number
+and do not count in their row.
 
 ## Output formats
 
@@ -199,7 +201,7 @@ colour key:
 | Full shading (stripes/dots) | `shading:pattern:full` | Affected (2) |
 | Half colour fill (one side only) | `#rrggbb` | Carrier (3) |
 | Half shading | `shading:pattern:half-left` | Carrier (3) |
-| Quartered fill (any quarter) | `#rrggbb` | Affected (2) |
+| Thirds or quarters (any part) | `#rrggbb` | Affected (2) |
 | Centre dot (●) | — | Carrier (3) |
 | No fill | — | Unaffected (1) |
 

{studio2ped-0.2.0 → studio2ped-0.2.1}/README.md

@@ -76,11 +76,12 @@ The converter reads a Pedigree Studio session file and:
 4. **Gives genetic parents only.** The father and mother columns of a PED
    file are genetic parents. A child joined to a couple by a dashed line (an
    adoption) gets 0 for that couple, and so does the place of a parent marked
-   S (a gestational carrier), with a note in each case; a parent marked D (a
-   donor) is a genetic parent. studio2ga4gh's PED-style pedigree gives the
-   same.
+   G (a gestational carrier), with a note in each case; a parent marked D (a
+   donor) is a genetic parent. Drawings made before the 2025 correction to the
+   pedigree nomenclature mark a gestational carrier S, which is read the same
+   way. studio2ga4gh's PED-style pedigree gives the same.
 5. **Extracts phenotypes** from the colour key: solid fills, half fills,
-   quartered fills and shading patterns are all recognised.
+   symbols in thirds or quarters, and shading patterns are all recognised.
 6. **Detects carrier notation**: centre dots (●) and half-filled symbols mark
    carriers.
 7. **Chooses the format**:
@@ -113,9 +114,10 @@ would be `0`, the person is given their pedigree number instead, and a note
 says so.
 
 Pedigree numbers follow the drawing, as in Pedigree Studio: a new generation
-starts 80 pixels or more below the first symbol of the generation above, and
-the "no children" and "infertility" symbols are counted in their row, even
-though they are not written to the file.
+starts 80 pixels or more below the first person of the generation above, and
+each generation is numbered from the left. Only people are numbered: the "no
+children" and "infertility" symbols are not people, so they have no number
+and do not count in their row.
 
 ## Output formats
 
@@ -176,7 +178,7 @@ colour key:
 | Full shading (stripes/dots) | `shading:pattern:full` | Affected (2) |
 | Half colour fill (one side only) | `#rrggbb` | Carrier (3) |
 | Half shading | `shading:pattern:half-left` | Carrier (3) |
-| Quartered fill (any quarter) | `#rrggbb` | Affected (2) |
+| Thirds or quarters (any part) | `#rrggbb` | Affected (2) |
 | Centre dot (●) | — | Carrier (3) |
 | No fill | — | Unaffected (1) |
 

{studio2ped-0.2.0 → studio2ped-0.2.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "studio2ped"
-version = "0.2.0"
+version = "0.2.1"
 description = "Convert Pedigree Studio session JSON to PED/MPED pedigree files"
 readme = "README.md"
 license = "MIT"

{studio2ped-0.2.0 → studio2ped-0.2.1}/studio2ped/__init__.py

@@ -1,6 +1,6 @@
 """studio2ped — Convert Pedigree Studio session JSON to PED/MPED pedigree files."""
 
-__version__ = "0.2.0"
+__version__ = "0.2.1"
 
 from .converter import (  # noqa: E402
     ID_CHOICES, ConversionResult, convert, convert_file, individual_ids, parse_session, pedigree_numbers,

{studio2ped-0.2.0 → studio2ped-0.2.1}/studio2ped/converter.py

@@ -37,6 +37,12 @@ SHAPE_TO_SEX = {
 # couple, so they have to be taken out before the family is written.
 MARKERS = {"no-offspring": "no children", "infertile": "infertility"}
 
+# The marks inside a symbol that make someone a gestational carrier, who carried a
+# child but is not their genetic parent: G since the 2025 correction to the pedigree
+# nomenclature, and S, which drawings from before it use (a woman who gives the egg
+# and carries the pregnancy is a donor, D, and so a genetic parent)
+GESTATIONAL_CARRIER = ("G", "S")
+
 # The kinds of identifier --ids offers (see individual_ids)
 ID_CHOICES = ("numbers", "drawing", "studio", "text")
 
@@ -52,13 +58,14 @@ class Person:
     shape: str
     sex: int
     text: str                        # annotation text (may contain name, dob, etc.)
-    fill_mode: str                   # 'none'|'solid'|'half'|'quartered'|'shading'
+    fill_mode: str                   # 'none'|'solid'|'half'|'thirds'|'quartered'|'shading'
     fill_color: Optional[str]        # hex colour for solid fill
     halves: list                     # [left_colour|None, right_colour|None]
     quarters: list                   # [TR, BR, BL, TL] colours or None
+    thirds: list                     # [top right, bottom, top left] colours or None
     shading_pattern: str             # 'stripes'|'dots'
     shading_coverage: str            # 'full'|'half-left'|'half-right'
-    center_text: str                 # 'S'|'P'|'D'|'dot'|''
+    center_text: str                 # 'G'|'S'|'P'|'D'|'dot'|'line'|''
     deceased: bool
     custom_label: str
     father_id: Optional[str] = None  # the genetic parents, resolved during graph analysis
@@ -142,6 +149,7 @@ def parse_session(data: dict) -> tuple[dict[str, Person], list[Partnership], lis
             fill_color=pd.get("fillColor"),
             halves=pd.get("halves", [None, None]),
             quarters=pd.get("quarters", [None, None, None, None]),
+            thirds=pd.get("thirds") or [None, None, None],
             shading_pattern=pd.get("shadingPattern", "stripes"),
             shading_coverage=pd.get("shadingCoverage", "full"),
             center_text=pd.get("centerText", ""),
@@ -259,11 +267,13 @@ def resolve_parents(family: Family) -> list:
     ``drawn_father_id`` and ``drawn_mother_id`` are the couple the drawing
     joins a person to. ``father_id`` and ``mother_id`` are their genetic
     parents, which the PED file gives: a dashed line (an adoption) gives no
-    genetic parents, and a parent marked S, a gestational carrier (surrogate),
-    is not a genetic parent, as in studio2ga4gh's PED-style pedigree.
+    genetic parents, and a parent marked G, a gestational carrier, is not a
+    genetic parent, as in studio2ga4gh's PED-style pedigree. Drawings from
+    before the 2025 correction to the pedigree nomenclature mark a gestational
+    carrier S, which is read the same way.
 
     Returns what was not written as a parent, as ``("adopted", child, (a, b))``
-    and ``("surrogate", child, carrier, "mother" or "father")``.
+    and ``("gestational carrier", child, carrier, "mother" or "father")``.
     """
     pship_map = {p.id: p for p in family.partnerships}
     left_out = []
@@ -297,8 +307,8 @@ def resolve_parents(family: Family) -> list:
             left_out.append(("adopted", child.id, (p1.id, p2.id)))
             continue
         for parent, role in ((father, "father"), (mother, "mother")):
-            if parent.center_text == "S":
-                left_out.append(("surrogate", child.id, parent.id, role))
+            if parent.center_text in GESTATIONAL_CARRIER:
+                left_out.append(("gestational carrier", child.id, parent.id, role))
             elif role == "father":
                 child.father_id = parent.id
             else:
@@ -426,7 +436,7 @@ def classify_person_phenotypes(
     - Full shading matching a shading phenotype → affected (2)
     - Half fill with one half matching a colour phenotype → carrier (3)
     - Half shading matching a shading phenotype with half coverage → carrier (3)
-    - Quartered fill with any quarter matching a colour phenotype → affected (2)
+    - Thirds or quarters with any part matching a colour phenotype → affected (2)
     - Centre dot ('dot') → add carrier status for all phenotypes that person has
     - No matching fill → unaffected (1)
     """
@@ -451,11 +461,12 @@ def classify_person_phenotypes(
                 else:
                     is_half_colour[c] = False
 
-    elif person.fill_mode == "quartered":
-        for c in (person.quarters or []):
+    elif person.fill_mode in ("quartered", "thirds"):
+        # a symbol in thirds or quarters: one part for each condition, each affected
+        for c in ((person.quarters if person.fill_mode == "quartered" else person.thirds) or []):
             if c:
                 person_colours.add(c)
-                is_half_colour[c] = False  # quartered = affected
+                is_half_colour[c] = False
 
     # Match colour phenotypes
     for ph in phenotypes:
@@ -520,12 +531,13 @@ def has_carrier_notation(persons: dict[str, Person]) -> bool:
 def drawn_rows(persons: dict[str, Person]) -> list[list[Person]]:
     """The rows (generations) of the drawing as Pedigree Studio numbers them.
 
-    Everyone is sorted from top to bottom, the "no children" and "infertile"
-    symbols included; a new row starts 80 px or more below the first symbol of
-    the row above, and each row is read from left to right.
+    The people are sorted from top to bottom; a new row starts 80 px or more
+    below the first person of the row above, and each row is read from left to
+    right. The "no children" and "infertile" symbols are not people, so they
+    are left out and do not count in their row.
     """
     rows: list[list[Person]] = []
-    for p in sorted(persons.values(), key=lambda q: q.y):
+    for p in sorted((q for q in persons.values() if not q.is_marker), key=lambda q: q.y):
         if rows and p.y - rows[-1][0].y < 80:
             rows[-1].append(p)
         else:
@@ -539,7 +551,8 @@ def _generation_label(index: int) -> str:
 
 def pedigree_numbers(persons: dict[str, Person]) -> dict[str, str]:
     """Pedigree numbers as Pedigree Studio shows them: the generation in Roman
-    numerals and the position from the left, such as ``II-3``."""
+    numerals and the position from the left, such as ``II-3``. Only people are
+    numbered: the "no children" and "infertile" symbols have no number."""
     out = {}
     for gi, row in enumerate(drawn_rows(persons)):
         for pi, p in enumerate(row):
@@ -556,14 +569,17 @@ def _letters(n: int) -> str:
 
 
 def drawing_labels(persons: dict[str, Person], numbering_mode: str = "numbers") -> dict[str, str]:
-    """The label each symbol shows in the drawing under its numbering setting:
+    """The label each person shows in the drawing under its numbering setting:
     pedigree numbers (``numbers``, and ``off``), letters (``letters``: II-A;
     ``lettersonly``: A, B, C ...) or the labels typed in (``freetext``, where a
-    symbol without one shows its pedigree number)."""
+    person without one shows their pedigree number). The "no children" and
+    "infertile" symbols have no label."""
     numbers = pedigree_numbers(persons)
     if numbering_mode == "freetext":
         out = {}
         for pid, p in persons.items():
+            if p.is_marker:
+                continue
             label = (p.custom_label or "").strip()
             out[pid] = label if label and label != "Lbl" else numbers[pid]
         return out
@@ -598,8 +614,9 @@ def individual_ids(
     * ``text``: version 0.1.0's identifiers (see :func:`make_individual_id`),
       which are often names.
 
-    ``persons`` should include the "no children" and "infertile" symbols,
-    because Pedigree Studio counts them when it numbers a row. Identifiers must
+    ``persons`` may include the "no children" and "infertile" symbols: they
+    are not people, so they are given no identifier and, as in Pedigree
+    Studio, do not count when a row is numbered. Identifiers must
     be unique, so anyone whose identifier would be shared with someone else, or
     would be empty or ``0`` (which PED reads as "no parent"), is given their
     pedigree number instead, and a note says so.
@@ -900,8 +917,9 @@ def convert(
                              f"parents are not genetic parents, so they are not written as {id_map[child]}'s parents")
             else:
                 _, child, carrier, role = item
-                notes.append(f"{id_map[carrier]} carried {id_map[child]} as a surrogate (S): a gestational carrier is "
-                             f"not a genetic parent, so {id_map[child]}'s {role} is written as 0")
+                mark = fam.persons[carrier].center_text
+                notes.append(f"{id_map[carrier]} carried {id_map[child]} as a gestational carrier ({mark}), and a "
+                             f"gestational carrier is not a genetic parent, so {id_map[child]}'s {role} is written as 0")
         assign_generations(fam)
 
     # Extract phenotypes from legend

{studio2ped-0.2.0 → studio2ped-0.2.1/studio2ped.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: studio2ped
-Version: 0.2.0
+Version: 0.2.1
 Summary: Convert Pedigree Studio session JSON to PED/MPED pedigree files
 Author-email: Tim Hearn <tjh70@cam.ac.uk>
 License-Expression: MIT
@@ -99,11 +99,12 @@ The converter reads a Pedigree Studio session file and:
 4. **Gives genetic parents only.** The father and mother columns of a PED
    file are genetic parents. A child joined to a couple by a dashed line (an
    adoption) gets 0 for that couple, and so does the place of a parent marked
-   S (a gestational carrier), with a note in each case; a parent marked D (a
-   donor) is a genetic parent. studio2ga4gh's PED-style pedigree gives the
-   same.
+   G (a gestational carrier), with a note in each case; a parent marked D (a
+   donor) is a genetic parent. Drawings made before the 2025 correction to the
+   pedigree nomenclature mark a gestational carrier S, which is read the same
+   way. studio2ga4gh's PED-style pedigree gives the same.
 5. **Extracts phenotypes** from the colour key: solid fills, half fills,
-   quartered fills and shading patterns are all recognised.
+   symbols in thirds or quarters, and shading patterns are all recognised.
 6. **Detects carrier notation**: centre dots (●) and half-filled symbols mark
    carriers.
 7. **Chooses the format**:
@@ -136,9 +137,10 @@ would be `0`, the person is given their pedigree number instead, and a note
 says so.
 
 Pedigree numbers follow the drawing, as in Pedigree Studio: a new generation
-starts 80 pixels or more below the first symbol of the generation above, and
-the "no children" and "infertility" symbols are counted in their row, even
-though they are not written to the file.
+starts 80 pixels or more below the first person of the generation above, and
+each generation is numbered from the left. Only people are numbered: the "no
+children" and "infertility" symbols are not people, so they have no number
+and do not count in their row.
 
 ## Output formats
 
@@ -199,7 +201,7 @@ colour key:
 | Full shading (stripes/dots) | `shading:pattern:full` | Affected (2) |
 | Half colour fill (one side only) | `#rrggbb` | Carrier (3) |
 | Half shading | `shading:pattern:half-left` | Carrier (3) |
-| Quartered fill (any quarter) | `#rrggbb` | Affected (2) |
+| Thirds or quarters (any part) | `#rrggbb` | Affected (2) |
 | Centre dot (●) | — | Carrier (3) |
 | No fill | — | Unaffected (1) |
 

{studio2ped-0.2.0 → studio2ped-0.2.1}/studio2ped_standalone.py

@@ -2,7 +2,7 @@
 """
 studio2ped_standalone.py - Convert Pedigree Studio session JSON to PED/MPED files.
 
-Standalone single-file script: studio2ped 0.2.0 in one file, so no
+Standalone single-file script: studio2ped 0.2.1 in one file, so no
 installation is required - it needs only Python 3.9+.
 
 Usage:
@@ -23,7 +23,7 @@ from collections import Counter, defaultdict
 from dataclasses import dataclass, field
 from typing import Optional
 
-__version__ = "0.2.0"
+__version__ = "0.2.1"
 
 # ── PED phenotype codes ───────────────────────────────────────────────────
 PHENO_UNKNOWN = 0
@@ -43,6 +43,12 @@ SHAPE_TO_SEX = {
 # couple, so they have to be taken out before the family is written.
 MARKERS = {"no-offspring": "no children", "infertile": "infertility"}
 
+# The marks inside a symbol that make someone a gestational carrier, who carried a
+# child but is not their genetic parent: G since the 2025 correction to the pedigree
+# nomenclature, and S, which drawings from before it use (a woman who gives the egg
+# and carries the pregnancy is a donor, D, and so a genetic parent)
+GESTATIONAL_CARRIER = ("G", "S")
+
 # The kinds of identifier --ids offers (see individual_ids)
 ID_CHOICES = ("numbers", "drawing", "studio", "text")
 
@@ -58,13 +64,14 @@ class Person:
     shape: str
     sex: int
     text: str                        # annotation text (may contain name, dob, etc.)
-    fill_mode: str                   # 'none'|'solid'|'half'|'quartered'|'shading'
+    fill_mode: str                   # 'none'|'solid'|'half'|'thirds'|'quartered'|'shading'
     fill_color: Optional[str]        # hex colour for solid fill
     halves: list                     # [left_colour|None, right_colour|None]
     quarters: list                   # [TR, BR, BL, TL] colours or None
+    thirds: list                     # [top right, bottom, top left] colours or None
     shading_pattern: str             # 'stripes'|'dots'
     shading_coverage: str            # 'full'|'half-left'|'half-right'
-    center_text: str                 # 'S'|'P'|'D'|'dot'|''
+    center_text: str                 # 'G'|'S'|'P'|'D'|'dot'|'line'|''
     deceased: bool
     custom_label: str
     father_id: Optional[str] = None  # the genetic parents, resolved during graph analysis
@@ -148,6 +155,7 @@ def parse_session(data: dict) -> tuple[dict[str, Person], list[Partnership], lis
             fill_color=pd.get("fillColor"),
             halves=pd.get("halves", [None, None]),
             quarters=pd.get("quarters", [None, None, None, None]),
+            thirds=pd.get("thirds") or [None, None, None],
             shading_pattern=pd.get("shadingPattern", "stripes"),
             shading_coverage=pd.get("shadingCoverage", "full"),
             center_text=pd.get("centerText", ""),
@@ -265,11 +273,13 @@ def resolve_parents(family: Family) -> list:
     ``drawn_father_id`` and ``drawn_mother_id`` are the couple the drawing
     joins a person to. ``father_id`` and ``mother_id`` are their genetic
     parents, which the PED file gives: a dashed line (an adoption) gives no
-    genetic parents, and a parent marked S, a gestational carrier (surrogate),
-    is not a genetic parent, as in studio2ga4gh's PED-style pedigree.
+    genetic parents, and a parent marked G, a gestational carrier, is not a
+    genetic parent, as in studio2ga4gh's PED-style pedigree. Drawings from
+    before the 2025 correction to the pedigree nomenclature mark a gestational
+    carrier S, which is read the same way.
 
     Returns what was not written as a parent, as ``("adopted", child, (a, b))``
-    and ``("surrogate", child, carrier, "mother" or "father")``.
+    and ``("gestational carrier", child, carrier, "mother" or "father")``.
     """
     pship_map = {p.id: p for p in family.partnerships}
     left_out = []
@@ -303,8 +313,8 @@ def resolve_parents(family: Family) -> list:
             left_out.append(("adopted", child.id, (p1.id, p2.id)))
             continue
         for parent, role in ((father, "father"), (mother, "mother")):
-            if parent.center_text == "S":
-                left_out.append(("surrogate", child.id, parent.id, role))
+            if parent.center_text in GESTATIONAL_CARRIER:
+                left_out.append(("gestational carrier", child.id, parent.id, role))
             elif role == "father":
                 child.father_id = parent.id
             else:
@@ -432,7 +442,7 @@ def classify_person_phenotypes(
     - Full shading matching a shading phenotype → affected (2)
     - Half fill with one half matching a colour phenotype → carrier (3)
     - Half shading matching a shading phenotype with half coverage → carrier (3)
-    - Quartered fill with any quarter matching a colour phenotype → affected (2)
+    - Thirds or quarters with any part matching a colour phenotype → affected (2)
     - Centre dot ('dot') → add carrier status for all phenotypes that person has
     - No matching fill → unaffected (1)
     """
@@ -457,11 +467,12 @@ def classify_person_phenotypes(
                 else:
                     is_half_colour[c] = False
 
-    elif person.fill_mode == "quartered":
-        for c in (person.quarters or []):
+    elif person.fill_mode in ("quartered", "thirds"):
+        # a symbol in thirds or quarters: one part for each condition, each affected
+        for c in ((person.quarters if person.fill_mode == "quartered" else person.thirds) or []):
             if c:
                 person_colours.add(c)
-                is_half_colour[c] = False  # quartered = affected
+                is_half_colour[c] = False
 
     # Match colour phenotypes
     for ph in phenotypes:
@@ -526,12 +537,13 @@ def has_carrier_notation(persons: dict[str, Person]) -> bool:
 def drawn_rows(persons: dict[str, Person]) -> list[list[Person]]:
     """The rows (generations) of the drawing as Pedigree Studio numbers them.
 
-    Everyone is sorted from top to bottom, the "no children" and "infertile"
-    symbols included; a new row starts 80 px or more below the first symbol of
-    the row above, and each row is read from left to right.
+    The people are sorted from top to bottom; a new row starts 80 px or more
+    below the first person of the row above, and each row is read from left to
+    right. The "no children" and "infertile" symbols are not people, so they
+    are left out and do not count in their row.
     """
     rows: list[list[Person]] = []
-    for p in sorted(persons.values(), key=lambda q: q.y):
+    for p in sorted((q for q in persons.values() if not q.is_marker), key=lambda q: q.y):
         if rows and p.y - rows[-1][0].y < 80:
             rows[-1].append(p)
         else:
@@ -545,7 +557,8 @@ def _generation_label(index: int) -> str:
 
 def pedigree_numbers(persons: dict[str, Person]) -> dict[str, str]:
     """Pedigree numbers as Pedigree Studio shows them: the generation in Roman
-    numerals and the position from the left, such as ``II-3``."""
+    numerals and the position from the left, such as ``II-3``. Only people are
+    numbered: the "no children" and "infertile" symbols have no number."""
     out = {}
     for gi, row in enumerate(drawn_rows(persons)):
         for pi, p in enumerate(row):
@@ -562,14 +575,17 @@ def _letters(n: int) -> str:
 
 
 def drawing_labels(persons: dict[str, Person], numbering_mode: str = "numbers") -> dict[str, str]:
-    """The label each symbol shows in the drawing under its numbering setting:
+    """The label each person shows in the drawing under its numbering setting:
     pedigree numbers (``numbers``, and ``off``), letters (``letters``: II-A;
     ``lettersonly``: A, B, C ...) or the labels typed in (``freetext``, where a
-    symbol without one shows its pedigree number)."""
+    person without one shows their pedigree number). The "no children" and
+    "infertile" symbols have no label."""
     numbers = pedigree_numbers(persons)
     if numbering_mode == "freetext":
         out = {}
         for pid, p in persons.items():
+            if p.is_marker:
+                continue
             label = (p.custom_label or "").strip()
             out[pid] = label if label and label != "Lbl" else numbers[pid]
         return out
@@ -604,8 +620,9 @@ def individual_ids(
     * ``text``: version 0.1.0's identifiers (see :func:`make_individual_id`),
       which are often names.
 
-    ``persons`` should include the "no children" and "infertile" symbols,
-    because Pedigree Studio counts them when it numbers a row. Identifiers must
+    ``persons`` may include the "no children" and "infertile" symbols: they
+    are not people, so they are given no identifier and, as in Pedigree
+    Studio, do not count when a row is numbered. Identifiers must
     be unique, so anyone whose identifier would be shared with someone else, or
     would be empty or ``0`` (which PED reads as "no parent"), is given their
     pedigree number instead, and a note says so.
@@ -906,8 +923,9 @@ def convert(
                              f"parents are not genetic parents, so they are not written as {id_map[child]}'s parents")
             else:
                 _, child, carrier, role = item
-                notes.append(f"{id_map[carrier]} carried {id_map[child]} as a surrogate (S): a gestational carrier is "
-                             f"not a genetic parent, so {id_map[child]}'s {role} is written as 0")
+                mark = fam.persons[carrier].center_text
+                notes.append(f"{id_map[carrier]} carried {id_map[child]} as a gestational carrier ({mark}), and a "
+                             f"gestational carrier is not a genetic parent, so {id_map[child]}'s {role} is written as 0")
         assign_generations(fam)
 
     # Extract phenotypes from legend

{studio2ped-0.2.0 → studio2ped-0.2.1}/tests/test_studio2ped.py

@@ -66,16 +66,19 @@ def test_people_are_given_their_pedigree_numbers():
 
 
 def test_numbers_follow_pedigree_studio():
-    """A new generation starts 80 px or more below the first symbol of the one above; each generation is
-    numbered from the left, counting the "no children" and "infertile" symbols, as Pedigree Studio does."""
+    """A new generation starts 80 px or more below the first person of the one above; each generation is
+    numbered from the left. The "no children" and "infertile" symbols are not people: as in Pedigree Studio,
+    they have no number and do not count in their row."""
     session = {"persons": [
         person("a", x=300, y=100), person("b", "female", x=100, y=150),     # 50 px lower: still generation I
         person("c", x=200, y=179),                                         # 79 px below a: still I
         person("d", "female", x=50, y=180),                                # 80 px below a: generation II
         person("m", "no-offspring", x=10, y=200), person("e", x=400, y=210),
+        person("n", "infertile", x=20, y=300),                             # a row with only a bar is no generation
+        person("f", x=30, y=390),
     ], "partnerships": [], "childLinks": []}
     numbers = studio2ped.pedigree_numbers(studio2ped.parse_session(session)[0])
-    assert numbers == {"b": "I-1", "c": "I-2", "a": "I-3", "m": "II-1", "d": "II-2", "e": "II-3"}
+    assert numbers == {"b": "I-1", "c": "I-2", "a": "I-3", "d": "II-1", "e": "II-2", "f": "III-1"}
     deep = {"persons": [person("p{}".format(i), y=i * 100) for i in range(14)], "partnerships": [], "childLinks": []}
     numbers = studio2ped.pedigree_numbers(studio2ped.parse_session(deep)[0])
     assert numbers["p11"] == "XII-1" and numbers["p12"] == "13-1"
@@ -106,6 +109,26 @@ def test_ids_text_gives_version_0_1_0s_identifiers():
     assert any("'26'" in n and "IV-1 and IV-3" in n for n in result.notes)
 
 
+def test_the_bars_have_no_label_in_any_numbering():
+    """Letters, and labels typed in, skip the "no children" and "infertile" symbols as numbers do."""
+    session = {"persons": [
+        person("f", x=100, y=0), person("m", "female", x=200, y=0),
+        person("bar", "no-offspring", x=0, y=150, customLabel="from an older drawing"),
+        person("c1", x=100, y=150, customLabel="Kid"), person("c2", "female", x=200, y=150),
+    ], "partnerships": [{"id": "pr", "fromId": "f", "toId": "m"}],
+        "childLinks": [{"id": "l1", "partnershipId": "pr", "childId": "c1"},
+                       {"id": "l2", "partnershipId": "pr", "childId": "c2"}]}
+    ids = {mode: studio2ped.convert(dict(session, numberingMode=mode), ids="drawing").ids
+           for mode in ("numbers", "letters", "lettersonly", "freetext")}
+    assert ids["numbers"] == {"f": "I-1", "m": "I-2", "c1": "II-1", "c2": "II-2"}
+    assert ids["letters"] == {"f": "I-A", "m": "I-B", "c1": "II-A", "c2": "II-B"}
+    assert ids["lettersonly"] == {"f": "A", "m": "B", "c1": "C", "c2": "D"}
+    assert ids["freetext"] == {"f": "I-1", "m": "I-2", "c1": "Kid", "c2": "II-2"}
+    from studio2ped.converter import drawing_labels
+    everyone = studio2ped.parse_session(dict(session, numberingMode="freetext"))[0]
+    assert "bar" not in drawing_labels(everyone, "freetext") and "bar" not in drawing_labels(everyone, "letters")
+
+
 def test_ids_studio_and_drawing():
     session = load("okafor")
     studio_ids = studio2ped.convert(session, ids="studio").ids
@@ -180,7 +203,7 @@ def test_adoptive_and_surrogate_parents_are_not_genetic_parents():
     assert table["III-1"][2:4] == ["II-2", "0"]        # II-3, the mother in the drawing, is a surrogate
     assert table["III-3"][2:4] == ["0", "0"]           # adopted by II-6 and II-7
     assert table["III-2"][2:4] == ["II-5", "II-4"]     # a donor (D) is a genetic parent
-    assert any("II-3 carried III-1 as a surrogate" in n for n in features.notes)
+    assert any("II-3 carried III-1 as a gestational carrier (S)" in n for n in features.notes)
     assert any("II-6 and II-7 adopted III-3" in n for n in features.notes)
     ids = [r[1] for r in rows(features.files[0][1])]
     assert ids.index("III-3") > ids.index("II-7")       # still listed with their generation
@@ -188,6 +211,36 @@ def test_adoptive_and_surrogate_parents_are_not_genetic_parents():
     assert {r[1]: r for r in rows(price.files[0][1])}["III-5"][2:4] == ["0", "0"]
 
 
+def test_a_parent_marked_g_is_a_gestational_carrier():
+    """Since the 2025 correction to the nomenclature, Pedigree Studio marks a gestational carrier G: read as S was."""
+    session = load("features")
+    marked = [p for p in session["persons"] if p.get("centerText") == "S"]
+    assert len(marked) == 1
+    marked[0]["centerText"] = "G"
+    features = studio2ped.convert(session)
+    table = {r[1]: r for r in rows(features.files[0][1])}
+    assert table["III-1"][2:4] == ["II-2", "0"]        # II-3, the mother in the drawing, is the gestational carrier
+    assert any("II-3 carried III-1 as a gestational carrier (G)" in n for n in features.notes)
+    assert not any("surrogate" in n for n in features.notes)
+    assert studio2ped.convert(load("features")).files == features.files   # G and S give the same file
+
+
+def test_a_symbol_in_thirds_has_each_condition():
+    """Pedigree Studio can divide a symbol into thirds, one part for each of up to three conditions (Bennett et al.
+    2022): each colour in it is a condition the person has, as with quarters."""
+    session = {"persons": [person("p1", "male", 0, 0), person("p2", "female", 104, 0),
+                           person("p3", "male", 52, 130, fillMode="thirds", thirds=["#c0392b", "#2980b9", None]),
+                           person("p4", "female", 156, 130, fillMode="quartered", quarters=["#c0392b", None, None, None])],
+               "partnerships": [{"id": "ps1", "fromId": "p1", "toId": "p2"}],
+               "childLinks": [{"id": "c1", "partnershipId": "ps1", "childId": "p3"},
+                              {"id": "c2", "partnershipId": "ps1", "childId": "p4"}],
+               "legendLabels": {"#c0392b": "Condition A", "#2980b9": "Condition B"}}
+    table = {r[1]: r for r in rows(studio2ped.convert(session).files[0][1])}
+    assert table["II-1"][5:] == ["2", "2"]
+    assert table["II-2"][5:] == ["2", "1"]
+    assert table["I-1"][5:] == ["1", "1"]
+
+
 def test_labels_become_identifiers_as_in_studio2ga4gh():
     """Spaces become underscores and other punctuation is dropped, the same rule studio2ga4gh uses, so a person
     has the same identifier in the PED file and the GA4GH files."""