From 9a71318c57229a7aa9668e777a4e3b4d29d1c677 Mon Sep 17 00:00:00 2001
From: VsevolodX <vsevolodbiryukov@icloud.com>
Date: Tue, 9 Jun 2026 11:37:02 -0700
Subject: [PATCH 1/5] update: fortran in js

---
 dist/js/shared/str.d.ts | 2 +-
 dist/js/shared/str.js   | 3 ++-
 src/js/shared/str.js    | 3 ++-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/dist/js/shared/str.d.ts b/dist/js/shared/str.d.ts
index bcda43c..d3f91f9 100644
--- a/dist/js/shared/str.d.ts
+++ b/dist/js/shared/str.d.ts
@@ -7,7 +7,7 @@ export function removeNewLinesAndExtraSpaces(str: any): any;
 export function randomAlphanumeric(length: number): string;
 export function toFixedLocale(number: any, precision: any): any;
 /**
- * @summary Removes full-line and inline comments starting with #. Shebang (#!) is excluded.
+ * @summary Removes comments from a given source code text based on the specified programming language.
  * @param text {String} text to remove comments from.
  * @param language {String} programming language of the text.
  * @return {String}
diff --git a/dist/js/shared/str.js b/dist/js/shared/str.js
index a47b9db..5b2fde7 100644
--- a/dist/js/shared/str.js
+++ b/dist/js/shared/str.js
@@ -40,7 +40,7 @@ function toFixedLocale(number, precision) {
 }
 exports.toFixedLocale = toFixedLocale;
 /**
- * @summary Removes full-line and inline comments starting with #. Shebang (#!) is excluded.
+ * @summary Removes comments from a given source code text based on the specified programming language.
  * @param text {String} text to remove comments from.
  * @param language {String} programming language of the text.
  * @return {String}
@@ -48,6 +48,7 @@ exports.toFixedLocale = toFixedLocale;
 function removeCommentsFromSourceCode(text, language = "shell") {
     const regexList = {
         shell: /#(?!!).*$/gm,
+        fortran: /!.*$/gm,
     };
     return text.replace(regexList[language], "");
 }
diff --git a/src/js/shared/str.js b/src/js/shared/str.js
index b5dd7f9..5529114 100644
--- a/src/js/shared/str.js
+++ b/src/js/shared/str.js
@@ -37,7 +37,7 @@ export function toFixedLocale(number, precision) {
 }
 
 /**
- * @summary Removes full-line and inline comments starting with #. Shebang (#!) is excluded.
+ * @summary Removes comments from a given source code text based on the specified programming language.
  * @param text {String} text to remove comments from.
  * @param language {String} programming language of the text.
  * @return {String}
@@ -45,6 +45,7 @@ export function toFixedLocale(number, precision) {
 export function removeCommentsFromSourceCode(text, language = "shell") {
     const regexList = {
         shell: /#(?!!).*$/gm,
+        fortran: /!.*$/gm,
     };
     return text.replace(regexList[language], "");
 }

From bc3dfb1191f35df1c16f14b4b81edc827650e8e2 Mon Sep 17 00:00:00 2001
From: VsevolodX <vsevolodbiryukov@icloud.com>
Date: Tue, 9 Jun 2026 12:23:05 -0700
Subject: [PATCH 2/5] update: sync py and js

---
 dist/js/shared/str.js         | 5 +++--
 src/js/shared/str.js          | 4 ++--
 src/py/mat3ra/utils/string.py | 2 +-
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/dist/js/shared/str.js b/dist/js/shared/str.js
index 5b2fde7..f8ebf52 100644
--- a/dist/js/shared/str.js
+++ b/dist/js/shared/str.js
@@ -46,11 +46,12 @@ exports.toFixedLocale = toFixedLocale;
  * @return {String}
  */
 function removeCommentsFromSourceCode(text, language = "shell") {
+    var _a;
     const regexList = {
         shell: /#(?!!).*$/gm,
-        fortran: /!.*$/gm,
+        fortran: /[!#].*$/gm,
     };
-    return text.replace(regexList[language], "");
+    return text.replace((_a = regexList[language]) !== null && _a !== void 0 ? _a : regexList.shell, "");
 }
 exports.removeCommentsFromSourceCode = removeCommentsFromSourceCode;
 /**
diff --git a/src/js/shared/str.js b/src/js/shared/str.js
index 5529114..6c1567d 100644
--- a/src/js/shared/str.js
+++ b/src/js/shared/str.js
@@ -45,9 +45,9 @@ export function toFixedLocale(number, precision) {
 export function removeCommentsFromSourceCode(text, language = "shell") {
     const regexList = {
         shell: /#(?!!).*$/gm,
-        fortran: /!.*$/gm,
+        fortran: /[!#].*$/gm,
     };
-    return text.replace(regexList[language], "");
+    return text.replace(regexList[language] ?? regexList.shell, "");
 }
 
 /**
diff --git a/src/py/mat3ra/utils/string.py b/src/py/mat3ra/utils/string.py
index 5c68b75..56b9589 100644
--- a/src/py/mat3ra/utils/string.py
+++ b/src/py/mat3ra/utils/string.py
@@ -64,7 +64,7 @@ def remove_comments_from_source_code(text: str, language: str = "shell") -> str:
     TODO: consider preserving values enclosed in quotes
     """
     if language == "fortran":
-        # Removes inline and full-line comments starting with ! or #
+        # Removes inline and full-line comments starting with ! or # (QE input uses both)
         return re.sub(r"[!#].*$", "", text, flags=re.MULTILINE)
 
     # Default (shell): removes inline and full-line # comments (except shebang)

From 0f56847954c5a3ba7fb4340c6e1b5d4cbd8a86f2 Mon Sep 17 00:00:00 2001
From: VsevolodX <vsevolodbiryukov@icloud.com>
Date: Wed, 10 Jun 2026 10:22:26 -0700
Subject: [PATCH 3/5] update: add python

---
 dist/js/shared/str.d.ts         |  6 ++++++
 dist/js/shared/str.js           | 14 ++++++++++++--
 src/js/shared/str.js            | 12 +++++++++++-
 src/py/mat3ra/utils/__init__.py |  2 +-
 src/py/mat3ra/utils/string.py   | 14 ++++++++++----
 5 files changed, 40 insertions(+), 8 deletions(-)

diff --git a/dist/js/shared/str.d.ts b/dist/js/shared/str.d.ts
index d3f91f9..df37470 100644
--- a/dist/js/shared/str.d.ts
+++ b/dist/js/shared/str.d.ts
@@ -13,6 +13,12 @@ export function toFixedLocale(number: any, precision: any): any;
  * @return {String}
  */
 export function removeCommentsFromSourceCode(text: string, language?: string): string;
+/**
+ * @summary Removes comments from Quantum ESPRESSO input (Fortran ! then Python #).
+ * @param text {String} text to remove comments from.
+ * @return {String}
+ */
+export function removeCommentsQe(text: string): string;
 /**
  * @summary Removes empty lines from a given string.
  * @param string {String} string to remove empty lines from.
diff --git a/dist/js/shared/str.js b/dist/js/shared/str.js
index f8ebf52..07d18c6 100644
--- a/dist/js/shared/str.js
+++ b/dist/js/shared/str.js
@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.numberFormat = exports.numberPadArray = exports.numberPad = exports.createSafeFilename = exports.renderTemplateStringWithEval = exports.renderTemplateString = exports.findPreviousVersion = exports.convertArabicToRoman = exports.removeEmptyLinesFromString = exports.removeCommentsFromSourceCode = exports.toFixedLocale = exports.randomAlphanumeric = exports.removeNewLinesAndExtraSpaces = void 0;
+exports.numberFormat = exports.numberPadArray = exports.numberPad = exports.createSafeFilename = exports.renderTemplateStringWithEval = exports.renderTemplateString = exports.findPreviousVersion = exports.convertArabicToRoman = exports.removeEmptyLinesFromString = exports.removeCommentsQe = exports.removeCommentsFromSourceCode = exports.toFixedLocale = exports.randomAlphanumeric = exports.removeNewLinesAndExtraSpaces = void 0;
 const coerce_1 = __importDefault(require("semver/functions/coerce"));
 const lt_1 = __importDefault(require("semver/functions/lt"));
 const rcompare_1 = __importDefault(require("semver/functions/rcompare"));
@@ -49,11 +49,21 @@ function removeCommentsFromSourceCode(text, language = "shell") {
     var _a;
     const regexList = {
         shell: /#(?!!).*$/gm,
-        fortran: /[!#].*$/gm,
+        fortran: /!.*$/gm,
+        python: /#.*$/gm,
     };
     return text.replace((_a = regexList[language]) !== null && _a !== void 0 ? _a : regexList.shell, "");
 }
 exports.removeCommentsFromSourceCode = removeCommentsFromSourceCode;
+/**
+ * @summary Removes comments from Quantum ESPRESSO input (Fortran ! then Python #).
+ * @param text {String} text to remove comments from.
+ * @return {String}
+ */
+function removeCommentsQe(text) {
+    return removeCommentsFromSourceCode(removeCommentsFromSourceCode(text, "fortran"), "python");
+}
+exports.removeCommentsQe = removeCommentsQe;
 /**
  * @summary Removes empty lines from a given string.
  * @param string {String} string to remove empty lines from.
diff --git a/src/js/shared/str.js b/src/js/shared/str.js
index 6c1567d..dff9814 100644
--- a/src/js/shared/str.js
+++ b/src/js/shared/str.js
@@ -45,11 +45,21 @@ export function toFixedLocale(number, precision) {
 export function removeCommentsFromSourceCode(text, language = "shell") {
     const regexList = {
         shell: /#(?!!).*$/gm,
-        fortran: /[!#].*$/gm,
+        fortran: /!.*$/gm,
+        python: /#.*$/gm,
     };
     return text.replace(regexList[language] ?? regexList.shell, "");
 }
 
+/**
+ * @summary Removes comments from Quantum ESPRESSO input (Fortran ! then Python #).
+ * @param text {String} text to remove comments from.
+ * @return {String}
+ */
+export function removeCommentsQe(text) {
+    return removeCommentsFromSourceCode(removeCommentsFromSourceCode(text, "fortran"), "python");
+}
+
 /**
  * @summary Removes empty lines from a given string.
  * @param string {String} string to remove empty lines from.
diff --git a/src/py/mat3ra/utils/__init__.py b/src/py/mat3ra/utils/__init__.py
index 3446458..873aa32 100644
--- a/src/py/mat3ra/utils/__init__.py
+++ b/src/py/mat3ra/utils/__init__.py
@@ -2,4 +2,4 @@
 from .string import camel_to_snake, snake_to_camel
 
 from .object import calculate_hash_from_object, remove_timestampable_keys, sort_keys_deep
-from .string import remove_comments_from_source_code, remove_empty_lines_from_string
+from .string import remove_comments_from_source_code, remove_comments_qe, remove_empty_lines_from_string
diff --git a/src/py/mat3ra/utils/string.py b/src/py/mat3ra/utils/string.py
index 56b9589..9bca372 100644
--- a/src/py/mat3ra/utils/string.py
+++ b/src/py/mat3ra/utils/string.py
@@ -64,13 +64,19 @@ def remove_comments_from_source_code(text: str, language: str = "shell") -> str:
     TODO: consider preserving values enclosed in quotes
     """
     if language == "fortran":
-        # Removes inline and full-line comments starting with ! or # (QE input uses both)
-        return re.sub(r"[!#].*$", "", text, flags=re.MULTILINE)
-
-    # Default (shell): removes inline and full-line # comments (except shebang)
+        return re.sub(r"!.*$", "", text, flags=re.MULTILINE)
+    if language == "python":
+        return re.sub(r"#.*$", "", text, flags=re.MULTILINE)
     return re.sub(r"#(?!!).*$", "", text, flags=re.MULTILINE)
 
 
+def remove_comments_qe(text: str) -> str:
+    return remove_comments_from_source_code(
+        remove_comments_from_source_code(text, language="fortran"),
+        language="python",
+    )
+
+
 def remove_empty_lines_from_string(text: str) -> str:
     """Removes empty lines and trims."""
     return re.sub(r"^\s*[\r\n]", "", text, flags=re.MULTILINE).strip()

From 35548a1c26ccc91c40ec7b029efe0bc06758a5ee Mon Sep 17 00:00:00 2001
From: VsevolodX <vsevolodbiryukov@icloud.com>
Date: Wed, 10 Jun 2026 10:24:03 -0700
Subject: [PATCH 4/5] chore: cleanup

---
 dist/js/shared/str.d.ts       |  6 ------
 dist/js/shared/str.js         | 11 +----------
 src/js/shared/str.js          |  8 --------
 src/py/mat3ra/utils/string.py |  7 -------
 4 files changed, 1 insertion(+), 31 deletions(-)

diff --git a/dist/js/shared/str.d.ts b/dist/js/shared/str.d.ts
index df37470..d3f91f9 100644
--- a/dist/js/shared/str.d.ts
+++ b/dist/js/shared/str.d.ts
@@ -13,12 +13,6 @@ export function toFixedLocale(number: any, precision: any): any;
  * @return {String}
  */
 export function removeCommentsFromSourceCode(text: string, language?: string): string;
-/**
- * @summary Removes comments from Quantum ESPRESSO input (Fortran ! then Python #).
- * @param text {String} text to remove comments from.
- * @return {String}
- */
-export function removeCommentsQe(text: string): string;
 /**
  * @summary Removes empty lines from a given string.
  * @param string {String} string to remove empty lines from.
diff --git a/dist/js/shared/str.js b/dist/js/shared/str.js
index 07d18c6..fdf859a 100644
--- a/dist/js/shared/str.js
+++ b/dist/js/shared/str.js
@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.numberFormat = exports.numberPadArray = exports.numberPad = exports.createSafeFilename = exports.renderTemplateStringWithEval = exports.renderTemplateString = exports.findPreviousVersion = exports.convertArabicToRoman = exports.removeEmptyLinesFromString = exports.removeCommentsQe = exports.removeCommentsFromSourceCode = exports.toFixedLocale = exports.randomAlphanumeric = exports.removeNewLinesAndExtraSpaces = void 0;
+exports.numberFormat = exports.numberPadArray = exports.numberPad = exports.createSafeFilename = exports.renderTemplateStringWithEval = exports.renderTemplateString = exports.findPreviousVersion = exports.convertArabicToRoman = exports.removeEmptyLinesFromString = exports.removeCommentsFromSourceCode = exports.toFixedLocale = exports.randomAlphanumeric = exports.removeNewLinesAndExtraSpaces = void 0;
 const coerce_1 = __importDefault(require("semver/functions/coerce"));
 const lt_1 = __importDefault(require("semver/functions/lt"));
 const rcompare_1 = __importDefault(require("semver/functions/rcompare"));
@@ -55,15 +55,6 @@ function removeCommentsFromSourceCode(text, language = "shell") {
     return text.replace((_a = regexList[language]) !== null && _a !== void 0 ? _a : regexList.shell, "");
 }
 exports.removeCommentsFromSourceCode = removeCommentsFromSourceCode;
-/**
- * @summary Removes comments from Quantum ESPRESSO input (Fortran ! then Python #).
- * @param text {String} text to remove comments from.
- * @return {String}
- */
-function removeCommentsQe(text) {
-    return removeCommentsFromSourceCode(removeCommentsFromSourceCode(text, "fortran"), "python");
-}
-exports.removeCommentsQe = removeCommentsQe;
 /**
  * @summary Removes empty lines from a given string.
  * @param string {String} string to remove empty lines from.
diff --git a/src/js/shared/str.js b/src/js/shared/str.js
index dff9814..058b0a1 100644
--- a/src/js/shared/str.js
+++ b/src/js/shared/str.js
@@ -51,14 +51,6 @@ export function removeCommentsFromSourceCode(text, language = "shell") {
     return text.replace(regexList[language] ?? regexList.shell, "");
 }
 
-/**
- * @summary Removes comments from Quantum ESPRESSO input (Fortran ! then Python #).
- * @param text {String} text to remove comments from.
- * @return {String}
- */
-export function removeCommentsQe(text) {
-    return removeCommentsFromSourceCode(removeCommentsFromSourceCode(text, "fortran"), "python");
-}
 
 /**
  * @summary Removes empty lines from a given string.
diff --git a/src/py/mat3ra/utils/string.py b/src/py/mat3ra/utils/string.py
index 9bca372..6bb4ccd 100644
--- a/src/py/mat3ra/utils/string.py
+++ b/src/py/mat3ra/utils/string.py
@@ -70,13 +70,6 @@ def remove_comments_from_source_code(text: str, language: str = "shell") -> str:
     return re.sub(r"#(?!!).*$", "", text, flags=re.MULTILINE)
 
 
-def remove_comments_qe(text: str) -> str:
-    return remove_comments_from_source_code(
-        remove_comments_from_source_code(text, language="fortran"),
-        language="python",
-    )
-
-
 def remove_empty_lines_from_string(text: str) -> str:
     """Removes empty lines and trims."""
     return re.sub(r"^\s*[\r\n]", "", text, flags=re.MULTILINE).strip()

From 450ffb678389e638d0e8be1cdb4a5af1113b5cd2 Mon Sep 17 00:00:00 2001
From: VsevolodX <vsevolodbiryukov@icloud.com>
Date: Wed, 10 Jun 2026 10:29:34 -0700
Subject: [PATCH 5/5] chore: cleanup

---
 src/py/mat3ra/utils/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/py/mat3ra/utils/__init__.py b/src/py/mat3ra/utils/__init__.py
index 873aa32..3446458 100644
--- a/src/py/mat3ra/utils/__init__.py
+++ b/src/py/mat3ra/utils/__init__.py
@@ -2,4 +2,4 @@
 from .string import camel_to_snake, snake_to_camel
 
 from .object import calculate_hash_from_object, remove_timestampable_keys, sort_keys_deep
-from .string import remove_comments_from_source_code, remove_comments_qe, remove_empty_lines_from_string
+from .string import remove_comments_from_source_code, remove_empty_lines_from_string